MolNFT v1 · #99611 · protein
Crystal structure of rpia-R5P complex
4M8L · Ribose-5-phosphate isomerase a: “Crystal structure of rpia-R5P complex”. X-ray diffraction, 3 ligands (ARF, 5RP, CL), 11 pockets (best druggability 0.56). MolNFT v1 #99611 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4M8L
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- A4IYN5
- Ligands
- ARF, 5RP, CL
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 220 | 35% helix, 29% strand | A4IYN5 |
| B, C | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 217 | 34% helix, 29% strand | A4IYN5 |
| D | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 218 | 34% helix, 29% strand | A4IYN5 |
Ligands and binding sites
- ARF · Formamide · ligand · 41 copies · chains A, C, B, D
- 5RP · Ribulose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.56 | 0.85 | 24 | empty |
| 2 | 86 | 0.51 | 0.84 | 21 | ARF |
| 3 | 99 | 0.50 | 0.82 | 26 | ARF |
| 4 | 106 | 0.50 | 0.81 | 24 | ARF |
| 5 | 76 | 0.39 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1302 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1267 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 224 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 A4IYN5
- Elsewhere: RCSB PDB 4M8L · PDBe 4M8L · UniProt A4IYN5
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