MolNFT v1 · #114913 · protein
Structure of human ribokinase crystallized with amppnp
5C3Y: “Structure of human ribokinase crystallized with amppnp”. X-ray diffraction, 2 ligands (AN2, NA), 20 pockets (best druggability 0.76). MolNFT v1 #114913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C3Y
- Type
- protein
- Length
- 3,742 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- Q9H477
- Ligands
- AN2, NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 306 | 38% helix, 24% strand | Q9H477 |
| B, G, J | Ribokinase (EC 2.7.1.15) | protein | 314 | 39% helix, 24% strand | Q9H477 |
| C | Ribokinase (EC 2.7.1.15) | protein | 313 | 39% helix, 24% strand | Q9H477 |
| D, E, H, L | Ribokinase (EC 2.7.1.15) | protein | 311 | 39% helix, 24% strand | Q9H477 |
| F, K | Ribokinase (EC 2.7.1.15) | protein | 312 | 39% helix, 24% strand | Q9H477 |
| I | Ribokinase (EC 2.7.1.15) | protein | 313 | 39% helix, 24% strand | Q9H477 |
Ligands and binding sites
- AN2 · Amp phosphoramidate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.76 | 0.78 | 126 | AN2, NA |
| 2 | 852 | 0.76 | 0.80 | 81 | empty |
| 3 | 1004 | 0.75 | 0.78 | 107 | empty |
| 4 | 522 | 0.67 | 0.78 | 57 | AN2, NA |
| 5 | 579 | 0.67 | 0.77 | 67 | AN2, NA |
Interfaces
14 interfaces between chains.
- E–F · 1299 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1290 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1272 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1269 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1267 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5C3Y · Structure of human ribokinase crystallized with AMPPNP · the same entry in another collection · chain L against L, 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 Q9H477
- Elsewhere: RCSB PDB 5C3Y · PDBe 5C3Y · UniProt Q9H477
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