MolNFT v1 · #114915 · protein
Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup
5C40: “Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup”. X-ray diffraction, 3 ligands (ACP, NA, PO4), 4 pockets (best druggability 0.67). MolNFT v1 #114915 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5C40
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- Q9H477
- Ligands
- ACP, NA, PO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 314 | 39% helix, 23% strand | Q9H477 |
| B | Ribokinase (EC 2.7.1.15) | protein | 312 | 38% helix, 23% strand | Q9H477 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.67 | 0.78 | 59 | ACP, NA |
| 2 | 503 | 0.67 | 0.78 | 60 | ACP, NA |
| 3 | 89 | 0.38 | 0.76 | 18 | empty |
| 4 | 61 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1245 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5C40 · Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H477 · AlphaFold monomer V2.0 prediction for ribokinase (Q9H477) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9H477
- Elsewhere: RCSB PDB 5C40 · PDBe 5C40 · UniProt Q9H477
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