MolNFT v1 · #112501 · protein
X-ray crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (ispc) from acinetobacter baumannii
4ZN6: “X-ray crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (ispc) from acinetobacter baumannii”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.75). MolNFT v1 #112501 on GenesisL1: 3D structure…
- PDB
- 4ZN6
- Type
- protein
- Length
- 780 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
- B7H1U5
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 392 | 48% helix, 16% strand | B7H1U5 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 388 | 47% helix, 16% strand | B7H1U5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.75 | 0.87 | 33 | empty |
| 2 | 505 | 0.64 | 0.77 | 67 | SO4 |
| 3 | 245 | 0.60 | 0.80 | 45 | empty |
| 4 | 293 | 0.56 | 0.76 | 45 | SO4 |
| 5 | 130 | 0.54 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1710 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4ZN6 · X-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from… · the same entry in another collection · chain A against A, TM-score 1.00
- B7H1U5 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain B 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 B7H1U5
- Elsewhere: RCSB PDB 4ZN6 · PDBe 4ZN6 · UniProt B7H1U5
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