MolNFT v1 · #82812 · protein
Structure of L-ribulose 3-epimerase
3VYL: “Structure of L-ribulose 3-epimerase”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.88). MolNFT v1 #82812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VYL
- Type
- protein
- Length
- 2,376 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribulose 3-epimerase
- EC
- 5.3.1.-
- UniProt
- N0DP12
- Ligands
- MN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L-ribulose 3-epimerase (EC 5.3.1.-) | protein | 297 | 47% helix, 13% strand | N0DP12 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.88 | 0.91 | 86 | MPD |
| 2 | 712 | 0.86 | 0.90 | 79 | MPD |
| 3 | 272 | 0.80 | 0.91 | 30 | MPD |
| 4 | 1113 | 0.78 | 0.80 | 105 | empty |
| 5 | 60 | 0.71 | 0.98 | 23 | empty |
Interfaces
18 interfaces between chains.
- A–D · 1497 Ų buried · 27 hydrogen bonds · protein-protein
- E–H · 1484 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1470 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1435 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1281 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3VYL · Structure of L-ribulose 3-epimerase · the same entry in another collection · chain A against A, TM-score 1.00
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 N0DP12
- Elsewhere: RCSB PDB 3VYL · PDBe 3VYL · UniProt N0DP12
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