MolNFT v1 · #168466 · protein
Structure of ribokinase from giardia lamblia
6WHJ: “Structure of ribokinase from giardia lamblia”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #168466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WHJ
- Type
- protein
- Length
- 1,304 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribokinase
- EC
- 2.7.1.15
- UniProt
- A8B6Y7
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribokinase (EC 2.7.1.15) | protein | 330 | 42% helix, 22% strand | A8B6Y7 |
| B | Ribokinase (EC 2.7.1.15) | protein | 335 | 41% helix, 21% strand | A8B6Y7 |
| C | Ribokinase (EC 2.7.1.15) | protein | 329 | 42% helix, 22% strand | A8B6Y7 |
| D | Ribokinase (EC 2.7.1.15) | protein | 310 | 43% helix, 23% strand | A8B6Y7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.77 | 0.80 | 84 | EDO |
| 2 | 598 | 0.72 | 0.80 | 63 | EDO |
| 3 | 624 | 0.71 | 0.79 | 65 | EDO |
| 4 | 359 | 0.60 | 0.77 | 47 | empty |
| 5 | 152 | 0.46 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1266 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1251 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WHJ · Structure of Ribokinase from Giardia lamblia · 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 A8B6Y7
- Elsewhere: RCSB PDB 6WHJ · PDBe 6WHJ · UniProt A8B6Y7
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