MolNFT v1 · #124861 · protein
1-deoxy-D-xylulose 5-phosphate reductoisomerase from vibrio vulnificus in complex with MN(2+)
5KRR: “1-deoxy-D-xylulose 5-phosphate reductoisomerase from vibrio vulnificus in complex with MN(2+)”. X-ray diffraction, 2 ligands (MN, CL), 6 pockets (best druggability 0.71). MolNFT v1 #124861 on GenesisL1: 3D structure, binding sites…
- PDB
- 5KRR
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- EC
- 1.1.1.267
- UniProt
- Q8DBF5
- Ligands
- MN, CL
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 391 | 51% helix, 15% strand | Q8DBF5 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 393 | 50% helix, 16% strand | Q8DBF5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.71 | 0.86 | 31 | EDO |
| 2 | 591 | 0.68 | 0.78 | 74 | EDO, MN |
| 3 | 401 | 0.61 | 0.77 | 65 | EDO, MN |
| 4 | 79 | 0.42 | 0.79 | 17 | empty |
| 5 | 103 | 0.39 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1629 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5KRR · 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DBF5 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8DBF5
- Elsewhere: RCSB PDB 5KRR · PDBe 5KRR · UniProt Q8DBF5
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