MolNFT v1 · #172005 · protein
Ribokinase from thermus species
6ZNX: “Ribokinase from thermus species”. X-ray diffraction, 1 ligand (ADP), 12 pockets (best druggability 0.74). MolNFT v1 #172005 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZNX
- Type
- protein
- Length
- 1,138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- A0A0B0SD75
- Ligands
- ADP
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 300 | 39% helix, 25% strand | A0A0B0SD75 |
| B | Ribokinase (EC 2.7.1.15) | protein | 292 | 39% helix, 25% strand | A0A0B0SD75 |
| C | Ribokinase (EC 2.7.1.15) | protein | 265 | 37% helix, 21% strand | A0A0B0SD75 |
| D | Ribokinase (EC 2.7.1.15) | protein | 281 | 40% helix, 20% strand | A0A0B0SD75 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.74 | 0.77 | 103 | ADP |
| 2 | 429 | 0.67 | 0.79 | 47 | ADP |
| 3 | 451 | 0.65 | 0.78 | 59 | ADP |
| 4 | 357 | 0.62 | 0.78 | 47 | ADP |
| 5 | 93 | 0.53 | 0.84 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 681 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 384 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZNX · Ribokinase from Thermus Species · the same entry in another collection · chain A against A, 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 A0A0B0SD75
- Elsewhere: RCSB PDB 6ZNX · PDBe 6ZNX · UniProt A0A0B0SD75
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