MolNFT v1 · #114916 · protein
Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup and with 4 protomers
5C41: “Crystal structure of human ribokinase in complex with amppcp in P21 spacegroup and with 4 protomers”. X-ray diffraction, 3 ligands (ACP, NA, PO4), 10 pockets (best druggability 0.74). MolNFT v1 #114916 on GenesisL1: 3D structure…
- PDB
- 5C41
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- 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
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribokinase (EC 2.7.1.15) | protein | 317 | 38% helix, 23% strand | Q9H477 |
| B | Ribokinase (EC 2.7.1.15) | protein | 310 | 39% helix, 24% strand | Q9H477 |
| D | Ribokinase (EC 2.7.1.15) | protein | 316 | 39% helix, 23% strand | Q9H477 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.74 | 0.83 | 53 | ACP, NA |
| 2 | 538 | 0.74 | 0.82 | 54 | ACP, NA |
| 3 | 568 | 0.68 | 0.78 | 68 | ACP, NA |
| 4 | 579 | 0.68 | 0.78 | 63 | ACP, NA |
| 5 | 277 | 0.59 | 0.78 | 30 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1232 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1225 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- Q9H477 · AlphaFold monomer V2.0 prediction for ribokinase (Q9H477) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 5C41 · PDBe 5C41 · UniProt Q9H477
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