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Crystal structures of D-psicose 3-epimerase with D-sorbose from clostridium cellulolyticum H10
Analyse Crystal structures of D-psicose 3-epimerase with D-sorbose from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VNM
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase domain protein tim barrel
- UniProt
- B8I944
- Ligands
- SDD, MN
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase domain protein tim barrel | protein | 289 | 49% helix, 14% strand | B8I944 |
| B, D | Xylose isomerase domain protein tim barrel | protein | 290 | 49% helix, 14% strand | B8I944 |
| C | Xylose isomerase domain protein tim barrel | protein | 288 | 48% helix, 14% strand | B8I944 |
Ligands and binding sites
- SDD · D-sorbose · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.86 | 98 | empty |
| 2 | 115 | 0.73 | 0.93 | 28 | SDD |
| 3 | 108 | 0.72 | 0.93 | 26 | SDD |
| 4 | 125 | 0.68 | 0.90 | 30 | SDD |
| 5 | 138 | 0.68 | 0.89 | 33 | SDD |
Interfaces
6 interfaces between chains.
- B–C · 1485 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1457 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 606 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VNM · Crystal structures of D-Psicose 3-epimerase with D-sorbose from Clostridium… · the same entry in another collection · chain D against D, TM-score 1.00
- B8I944 · AlphaFold monomer V2.0 prediction for D-psicose 3-epimerase (B8I944) · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B8I944
- Elsewhere: RCSB PDB 3VNM · PDBe 3VNM · UniProt B8I944
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