MolNFT v1 · #113892 · protein
Crystal structure of geodermatophilus obscurus L-ribose isomerase
5AVP: “Crystal structure of geodermatophilus obscurus L-ribose isomerase”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.68). MolNFT v1 #113892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AVP
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribose isomerase
- EC
- 5.3.1.-
- UniProt
- D2S5K0
- Ligands
- MN
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-ribose isomerase (EC 5.3.1.-) | protein | 240 | 21% helix, 31% strand | D2S5K0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.68 | 0.88 | 22 | empty |
| 2 | 117 | 0.66 | 0.89 | 21 | empty |
| 3 | 240 | 0.63 | 0.82 | 37 | MN |
| 4 | 434 | 0.62 | 0.77 | 43 | empty |
| 5 | 412 | 0.61 | 0.76 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2418 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2354 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 936 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 112 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5AVP · Crystal structure of Geodermatophilus obscurus L-ribose isomerase · 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 D2S5K0
- Elsewhere: RCSB PDB 5AVP · PDBe 5AVP · UniProt D2S5K0
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