MolNFT v1 · #82450 · protein
Crystal structures of D-psicose 3-epimerase with D-fructose from clostridium cellulolyticum H10
3VNK · Xylose isomerase domain protein tim barrel: “Crystal structures of D-psicose 3-epimerase with D-fructose from clostridium cellulolyticum H10”. X-ray diffraction, 2 ligands (FUD, MN), 19 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3VNK
- Type
- protein
- Length
- 1,155 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
- FUD, MN
- Pockets
- 19 · best druggability 0.86
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 | 290 | 49% helix, 14% strand | B8I944 |
| B, D | Xylose isomerase domain protein tim barrel | protein | 288 | 49% helix, 14% strand | B8I944 |
| C | Xylose isomerase domain protein tim barrel | protein | 289 | 48% helix, 14% strand | B8I944 |
Ligands and binding sites
- FUD · D-fructose · 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
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.86 | 0.87 | 81 | empty |
| 2 | 97 | 0.71 | 0.94 | 25 | FUD |
| 3 | 117 | 0.68 | 0.90 | 32 | FUD |
| 4 | 99 | 0.66 | 0.91 | 31 | FUD |
| 5 | 104 | 0.65 | 0.90 | 32 | FUD |
Interfaces
6 interfaces between chains.
- B–C · 1481 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 1474 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 623 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 589 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 220 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VNK · Crystal structures of D-Psicose 3-epimerase with D-fructose 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 D 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 3VNK · PDBe 3VNK · UniProt B8I944
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