MolNFT v1 · #156682 · protein
Crystal structure of ribose-5-phosphate isomerase from legionella pneumophila with bound substrate ribose-5-phosphate and product ribulose-5-phosphate
6MC0 · Ribose-5-phosphate isomerase a: “Crystal structure of ribose-5-phosphate isomerase from legionella pneumophila with bound substrate…”. X-ray diffraction, 3 ligands (R5P, 5RP, NA), 4 pockets (best druggability 0.40). MolNFT v1…
- PDB
- 6MC0
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- Q5ZZB7
- Ligands
- R5P, 5RP, NA
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 218 | 34% helix, 27% strand | Q5ZZB7 |
| B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 217 | 34% helix, 27% strand | Q5ZZB7 |
Ligands and binding sites
- R5P · Ribose-5-phosphate · ligand · chains A
- 5RP · Ribulose-5-phosphate · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.40 | 0.82 | 19 | 5RP |
| 2 | 71 | 0.36 | 0.78 | 27 | R5P |
| 3 | 54 | 0.31 | 0.76 | 15 | empty |
| 4 | 50 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1255 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6MC0 · Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZZB7 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (Q5ZZB7) · a predicted model of the same protein · chain B 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 Q5ZZB7
- Elsewhere: RCSB PDB 6MC0 · PDBe 6MC0 · UniProt Q5ZZB7
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