Difference between revisions of "AtomSets/Carbohydrate"

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= 'carbohydrate' atom set =
 
= 'carbohydrate' atom set =
 +
''(Updated to Jmol 16.1.9)''
 +
 +
Atoms are included in this set according to the name of the residue (group) they belong to:
 +
 
== Alphabetic ==
 
== Alphabetic ==
  
Line 9: Line 13:
  
 
[AHR] = alpha-L-arabinofuranose
 
[AHR] = alpha-L-arabinofuranose
 +
 +
[ALL] = beta-D-allopyranose
 +
 +
[AMU] = N-acetyl-beta-muramic acid
  
 
[ARA] = alpha-L-arabinopyranose
 
[ARA] = alpha-L-arabinopyranose
Line 51: Line 59:
  
 
[GUP] = alpha-L-gulopyranose
 
[GUP] = alpha-L-gulopyranose
 +
 +
[GXL] = alpha-L-galactopyranose
  
 
[LAT] = beta-lactose
 
[LAT] = beta-lactose
 +
 +
[LBT] = alpha-lactose
  
 
[LXC] = beta-L-xylopyranose
 
[LXC] = beta-L-xylopyranose
Line 68: Line 80:
 
[MTT] = maltotetraose
 
[MTT] = maltotetraose
  
−
[NAG] = N-acetylglucosamine = GlcNAc = 2-(acetylamino)-2-deoxy-beta-D-glucopyranose)
+
[NAG] = N-acetyl-beta-D-glucosamine = β-GlcNAc = 2-(acetylamino)-2-deoxy-beta-D-glucopyranose)  (see also NDG)
  
 
[NAN] = <sialic> obsolete, replaced with SIA
 
[NAN] = <sialic> obsolete, replaced with SIA
 +
 +
[NDG] = N-acetyl-alpha-D-glucosamine = &alpha;-GlcNAc = 2-(acetylamino)-2-deoxy-alpha-D-glucopyranose)  (see also NAG)
  
 
[NGA] = N-acetyl-beta-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-beta-D-galactopyranose  (see also A2G)
 
[NGA] = N-acetyl-beta-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-beta-D-galactopyranose  (see also A2G)
Line 87: Line 101:
  
 
[SLB] = 5-N-acetyl-beta-D-neuraminic acid  (see also SIA)
 
[SLB] = 5-N-acetyl-beta-D-neuraminic acid  (see also SIA)
 +
 +
[SOE] = &alpha;-L-sorbopyranose
 +
 +
[SOL] = L-sorbose
  
 
[SOR] = D-glucitol = D-sorbitol
 
[SOR] = D-glucitol = D-sorbitol
Line 101: Line 119:
  
 
== Cathegorized ==
 
== Cathegorized ==
−
=== Monosaccharides ===
+
<table>
 +
  <tr>
 +
    <th></th>
 +
    <th style="border-bottom:1px solid #09E;">linear</th>
 +
      <th style="border-bottom:1px solid #09E;">pyranose</th>
 +
      <th style="border-bottom:1px solid #09E;">furanose</th>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="2" style="border-bottom:1px solid #09E;">glucose</th>
 +
    <td></td>
 +
      <td>&alpha;-D-Glc<sub>p</sub> <br>[GLC]</td>
 +
      <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Glc<sub>p</sub><br>[BGC]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th style="border-bottom:1px solid #09E;">fructose</th>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Fru<sub>p</sub><br>[BDF]</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Fru<sub>f</sub><br>[FRU]</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="3" style="border-bottom:1px solid #09E;">galactose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-D-Gal<sub>p</sub><br>[GLA]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td>&nbsp;</td>
 +
    <td>&beta;-D-Gal<sub>p</sub><br>    [GAL]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&alpha;-L-Gal<sub>p</sub><br>    [GXL]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="2" style="border-bottom:1px solid #09E;">mannose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-D-Man<sub>p</sub><br>    [MAN]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Man<sub>p</sub><br>    [BMA]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="2" style="border-bottom:1px solid #09E;">ribose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-D-Rib<sub>f</sub><br>    [RIB]</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Rib<sub>p</sub><br>[RIP]</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-Rib<sub>f</sub><br>    [BDR]</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="4" style="border-bottom:1px solid #09E;">fucose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-D-Fuc<sub>p</sub><br>    [FCA]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td>&nbsp;</td>
 +
    <td>&beta;-D-Fuc<sub>p</sub><br>    [FCB]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-L-Fuc<sub>p</sub><br>    [FUC]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-L-Fuc<sub>p</sub><br>    [FUL]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="3" style="border-bottom:1px solid #09E;">xylose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-D-Xyl<sub>p</sub><br>    [XYS]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td>&nbsp;</td>
 +
    <td>&beta;-D-Xyl<sub>p</sub><br>    [XYP]</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-L-Xyl<sub>p</sub><br>    [LXC]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="2" style="border-bottom:1px solid #09E;">arabinose</th>
 +
    <td>&nbsp;</td>
 +
    <td>&alpha;-L-Ara<sub>p</sub><br>    [ARA]</td>
 +
    <td>&alpha;-L-Ara<sub>f</sub><br>[AHR]</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-L-Ara<sub>p</sub><br>    [ARB]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th style="border-bottom:1px solid #09E;">gulose</th>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&alpha;-L-Gul<sub>p</sub><br>    [GUP]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th style="border-bottom:1px solid #09E;">rhamnose</th>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&alpha;-L-Rha<sub>p</sub><br>    [RAM]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th rowspan="2" style="border-bottom:1px solid #09E;">sorbose</th>
 +
    <td>L-sorbose<br>    [SOL]    <br></td>
 +
    <td>&nbsp;</td>
 +
    <td>&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&alpha;-L-sorbopyranose<br>    [SOE]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
  <tr>
 +
    <th style="border-bottom:1px solid #09E;">allose</th>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
    <td style="border-bottom:1px solid #09E;">&beta;-D-allopyranose<br>    [ALL]</td>
 +
    <td style="border-bottom:1px solid #09E;">&nbsp;</td>
 +
  </tr>
 +
</table>
 +
 
 +
=== Amino sugars ===
 +
 
 +
[NDG] = &alpha;-GlcNAc = N-acetyl-&alpha;-D-glucosamine = 2-(acetylamino)-2-deoxy-&alpha;-D-glucopyranose
 +
 
 +
[NAG] = &beta;-GlcNAc = N-acetyl-&beta;-D-glucosamine = 2-(acetylamino)-2-deoxy-&beta;-D-glucopyranose
 +
 
 +
[A2G] = &alpha;-GalNAc = N-acetyl-&alpha;-D-galactosamine = 2-(acetylamino)-2-deoxy-&alpha;-D-galactopyranose
 +
 
 +
[NGA] = &beta;-GalNAc = N-acetyl-&beta;-D-galactosamine = 2-(acetylamino)-2-deoxy-&beta;-D-galactopyranose
 +
 
 +
=== Sugar alcohols ===
 +
[MTL] = D-mannitol
 +
 
 +
[SOR] = D-glucitol = D-sorbitol
 +
 
 +
[XYL] = D-xylitol
 +
 
 +
=== Sugar acids ===
 +
[GCU] = D-glucuronic acid = &alpha;-D-glucopyranuronic acid
 +
 
 +
[RHA] = 6-deoxy-mannose-1'-phosphate
 +
 
 +
[SIA] = &alpha;-NeuNAc = 5-N-acetyl-&alpha;-D-neuraminic acid
 +
 
 +
[SLB] = &beta;-NeuNAc = 5-N-acetyl-&beta;-D-neuraminic acid
 +
 
 +
[AMU] = N-acetyl-&beta;-muramic acid
  
 
=== Disaccharides ===
 
=== Disaccharides ===
 +
[MAL] = maltose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>
 +
 
[CBI] = cellobiose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>
 
[CBI] = cellobiose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>
 +
 +
[TRE] = trehalose = &alpha;-D-Glc<sub>p</sub>(1->1)&alpha;-D-Glc<sub>p</sub>
  
 
[MAB] = mannobiose = [&beta;-D-Man<sub>p</sub>(1->4)]<sub>2</sub>
 
[MAB] = mannobiose = [&beta;-D-Man<sub>p</sub>(1->4)]<sub>2</sub>
  
−
[MAL] = maltose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>
+
[LBT] = alpha-lactose = &beta;-D-Gal<sub>p</sub>(1->4)&alpha;-D-Glc<sub>p</sub>
 +
 
 +
[LAT] = beta-lactose = &beta;-D-Gal<sub>p</sub>(1->4)&beta;-D-Glc<sub>p</sub>
  
 
[SUC] = sucrose = &beta;-D-Fru<sub>f</sub>(2->1)&alpha;-D-Glc<sub>p</sub>
 
[SUC] = sucrose = &beta;-D-Fru<sub>f</sub>(2->1)&alpha;-D-Glc<sub>p</sub>
−
 
−
[TRE] = trehalose = &alpha;-D-Glc<sub>p</sub>(1->1)&alpha;-D-Glc<sub>p</sub>
 
  
 
=== Trisaccharides ===
 
=== Trisaccharides ===
−
[CT3] = beta-cellotriose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>3</sub>
+
[MLR] = maltotriose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>3</sub>
  
 
[CTR] = cellotriose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>&alpha;-D-Glc<sub>p</sub>
 
[CTR] = cellotriose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>2</sub>&alpha;-D-Glc<sub>p</sub>
  
−
[MLR] = maltotriose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>3</sub>
+
[CT3] = beta-cellotriose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>3</sub>
  
 
=== Tetrasaccharides ===
 
=== Tetrasaccharides ===
 +
[MTT] = maltotetraose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>4</sub>
 +
 
[CTT] = cellotetraose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>4</sub>
 
[CTT] = cellotetraose = [&beta;-D-Glc<sub>p</sub>(1->4)]<sub>4</sub>
  
−
[MTT] = maltotetraose = [&alpha;-D-Glc<sub>p</sub>(1->4)]<sub>4</sub>
+
== References ==
 +
* RCSB PDB [http://ligand-expo.rcsb.org/ld-search.html `Ligand Expo´ Chemical Component Search Tools]
 +
* [PDBe ligand dictionary https://www.ebi.ac.uk/pdbe-srv/pdbechem/]

Latest revision as of 18:02, 24 April 2023

'carbohydrate' atom set

(Updated to Jmol 16.1.9)

Atoms are included in this set according to the name of the residue (group) they belong to:

Alphabetic

[A2G] = N-acetyl-alpha-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-alpha-D-galactopyranose (see also NGA)

[AFL] = <fucose> obsolete, replaced with FUL

[AGC] = <glucose> obsolete, replaced with GLC

[AHR] = alpha-L-arabinofuranose

[ALL] = beta-D-allopyranose

[AMU] = N-acetyl-beta-muramic acid

[ARA] = alpha-L-arabinopyranose

[ARB] = beta-L-arabinopyranose

[BDF] = beta-D-fructopyranose (see also FRU)

[BDR] = beta-D-ribofuranose

[BGC] = beta-D-glucopyranose (see also GLC)

[BMA] = beta-D-mannopyranose (see also MAN)

[CBI] = cellobiose

[CT3] = beta-cellotriose

[CTR] = cellotriose

[CTT] = cellotetraose

[FCA] = alpha-D-fucose (see also FCB, FUC, FUL)

[FCB] = beta-D-fucose (see also FCA, FUC, FUL)

[FRU] = beta-D-fructofuranose (see also BDF)

[FUC] = alpha-L-fucose (see also FCA, FCB, FUL)

[FUL] = beta-L-fucose (see also FCA, FCB, FUC)

[GAL] = beta-D-galactopyranose (see also GLA)

[GCU] = alpha-D-glucopyranuronic acid (glucuronic acid)

[GLA] = alpha-D-galactopyranose (see also GAL)

[GLB] = <galactose> obsolete, replaced with GAL

[GLC] = alpha-D-glucopyranose (see also BGC)

[GUP] = alpha-L-gulopyranose

[GXL] = alpha-L-galactopyranose

[LAT] = beta-lactose

[LBT] = alpha-lactose

[LXC] = beta-L-xylopyranose

[MAB] = mannobiose

[MAL] = maltose

[MAN] = alpha-D-mannopyranose (see also BMA)

[MLR] = maltotriose

[MTL] = D-mannitol

[MTT] = maltotetraose

[NAG] = N-acetyl-beta-D-glucosamine = β-GlcNAc = 2-(acetylamino)-2-deoxy-beta-D-glucopyranose) (see also NDG)

[NAN] = <sialic> obsolete, replaced with SIA

[NDG] = N-acetyl-alpha-D-glucosamine = α-GlcNAc = 2-(acetylamino)-2-deoxy-alpha-D-glucopyranose) (see also NAG)

[NGA] = N-acetyl-beta-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-beta-D-galactopyranose (see also A2G)

[RAA] = <rhamnose> obsolete, replaced with RAM

[RAM] = alpha-L-rhamnose

[RHA] = 6-deoxy-mannose-1'-phosphate

[RIB] = alpha-D-ribofuranose

[RIP] = beta-D-ribopyranose

[SIA] = 5-N-acetyl-alpha-D-neuraminic acid (see also SLB)

[SLB] = 5-N-acetyl-beta-D-neuraminic acid (see also SIA)

[SOE] = α-L-sorbopyranose

[SOL] = L-sorbose

[SOR] = D-glucitol = D-sorbitol

[SUC] = sucrose

[TRE] = trehalose

[XYL] = D-xylitol

[XYP] = beta-D-xylopyranose

[XYS] = alpha-D-xylopyranose

Cathegorized

linear pyranose furanose
glucose α-D-Glcp
[GLC]		  
  β-D-Glcp
[BGC]		  
fructose   β-D-Frup
[BDF]		 β-D-Fruf
[FRU]
galactose   α-D-Galp
[GLA]		  
  β-D-Galp
[GAL]		  
  α-L-Galp
[GXL]		  
mannose   α-D-Manp
[MAN]		  
  β-D-Manp
[BMA]		  
ribose     α-D-Ribf
[RIB]
  β-D-Ribp
[RIP]		 β-D-Ribf
[BDR]
fucose   α-D-Fucp
[FCA]		  
  β-D-Fucp
[FCB]		  
  α-L-Fucp
[FUC]		  
  β-L-Fucp
[FUL]		  
xylose   α-D-Xylp
[XYS]		  
  β-D-Xylp
[XYP]		  
  β-L-Xylp
[LXC]		  
arabinose   α-L-Arap
[ARA]		 α-L-Araf
[AHR]
  β-L-Arap
[ARB]		  
gulose   α-L-Gulp
[GUP]		  
rhamnose   α-L-Rhap
[RAM]		  
sorbose L-sorbose
[SOL]
   
  α-L-sorbopyranose
[SOE]		  
allose   β-D-allopyranose
[ALL]		  

Amino sugars

[NDG] = α-GlcNAc = N-acetyl-α-D-glucosamine = 2-(acetylamino)-2-deoxy-α-D-glucopyranose

[NAG] = β-GlcNAc = N-acetyl-β-D-glucosamine = 2-(acetylamino)-2-deoxy-β-D-glucopyranose

[A2G] = α-GalNAc = N-acetyl-α-D-galactosamine = 2-(acetylamino)-2-deoxy-α-D-galactopyranose

[NGA] = β-GalNAc = N-acetyl-β-D-galactosamine = 2-(acetylamino)-2-deoxy-β-D-galactopyranose

Sugar alcohols

[MTL] = D-mannitol

[SOR] = D-glucitol = D-sorbitol

[XYL] = D-xylitol

Sugar acids

[GCU] = D-glucuronic acid = α-D-glucopyranuronic acid

[RHA] = 6-deoxy-mannose-1'-phosphate

[SIA] = α-NeuNAc = 5-N-acetyl-α-D-neuraminic acid

[SLB] = β-NeuNAc = 5-N-acetyl-β-D-neuraminic acid

[AMU] = N-acetyl-β-muramic acid

Disaccharides

[MAL] = maltose = [α-D-Glcp(1->4)]2

[CBI] = cellobiose = [β-D-Glcp(1->4)]2

[TRE] = trehalose = α-D-Glcp(1->1)α-D-Glcp

[MAB] = mannobiose = [β-D-Manp(1->4)]2

[LBT] = alpha-lactose = β-D-Galp(1->4)α-D-Glcp

[LAT] = beta-lactose = β-D-Galp(1->4)β-D-Glcp

[SUC] = sucrose = β-D-Fruf(2->1)α-D-Glcp

Trisaccharides

[MLR] = maltotriose = [α-D-Glcp(1->4)]3

[CTR] = cellotriose = [β-D-Glcp(1->4)]2α-D-Glcp

[CT3] = beta-cellotriose = [β-D-Glcp(1->4)]3

Tetrasaccharides

[MTT] = maltotetraose = [α-D-Glcp(1->4)]4

[CTT] = cellotetraose = [β-D-Glcp(1->4)]4

References

Contributors

AngelHerraez

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