MolNFT v1 · #13684 · protein
Structure of D-ribose-5-phosphate isomerase from in complex with phospho-erythronic acid
1LK7: “Structure of D-ribose-5-phosphate isomerase from in complex with phospho-erythronic acid”. X-ray diffraction, 3 ligands (DER, NA, CL), 15 pockets (best druggability 0.89). MolNFT v1 #13684 on GenesisL1: 3D structure, binding sites…
- PDB
- 1LK7
- 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
- DER, NA, CL
- Pockets
- 15 · 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
- DER · D-4-phosphoerythronic acid · ligand · 4 copies · chains A, C, B, D
- 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
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.89 | 0.91 | 106 | empty |
| 2 | 107 | 0.52 | 0.83 | 23 | CL, DER |
| 3 | 116 | 0.49 | 0.81 | 24 | CL, DER |
| 4 | 60 | 0.49 | 0.86 | 24 | CL, DER |
| 5 | 76 | 0.40 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1244 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1225 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1027 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1013 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1LK7 · Structure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid · 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 1LK7 · PDBe 1LK7 · UniProt O50083
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