MolNFT v1 · #13682 · protein
Structure of the D-ribose-5-phosphate isomerase from pyrococcus horikoshii
1LK5: “Structure of the D-ribose-5-phosphate isomerase from pyrococcus horikoshii”. X-ray diffraction, 2 ligands (NA, CL), 12 pockets (best druggability 0.89). MolNFT v1 #13682 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1LK5
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-ribose-5-phosphate isomerase
- EC
- 5.3.1.6
- UniProt
- O50083
- Ligands
- NA, CL
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-ribose-5-phosphate isomerase (EC 5.3.1.6) | protein | 229 | 34% helix, 28% strand | O50083 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, C, B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.89 | 0.91 | 112 | empty |
| 2 | 158 | 0.55 | 0.81 | 30 | CL |
| 3 | 79 | 0.52 | 0.86 | 23 | CL |
| 4 | 133 | 0.52 | 0.81 | 25 | CL |
| 5 | 113 | 0.50 | 0.82 | 25 | CL |
Interfaces
6 interfaces between chains.
- C–D · 1274 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1252 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1045 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1009 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 315 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1LK5 · Structure of the D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O50083 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (O50083) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O50083
- Elsewhere: RCSB PDB 1LK5 · PDBe 1LK5 · UniProt O50083
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