MolNFT v1 · #116985 · protein
1-deoxy-D-xylulose 5-phosphate reductoisomerase from yersinia pestis in complex with NADPH
5DUL: “1-deoxy-D-xylulose 5-phosphate reductoisomerase from yersinia pestis in complex with NADPH”. X-ray diffraction, 1 ligand (NDP), 12 pockets (best druggability 0.84). MolNFT v1 #116985 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DUL
- Type
- protein
- Length
- 1,519 residues
- Chains
- 4
- 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
- Q8ZH62
- Ligands
- NDP
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% 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 | 375 | 49% helix, 16% strand | Q8ZH62 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 390 | 49% helix, 16% strand | Q8ZH62 |
| C | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 367 | 49% helix, 16% strand | Q8ZH62 |
| D | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 387 | 49% helix, 16% strand | Q8ZH62 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.84 | 0.90 | 75 | empty |
| 2 | 1072 | 0.83 | 0.84 | 112 | empty |
| 3 | 498 | 0.82 | 0.89 | 62 | empty |
| 4 | 540 | 0.65 | 0.76 | 71 | NDP |
| 5 | 445 | 0.64 | 0.78 | 73 | NDP |
Interfaces
5 interfaces between chains.
- C–D · 1726 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 758 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 699 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DUL · 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis in complex with NADPH · the same entry in another collection · chain D against D, TM-score 1.00
- Q8ZH62 · 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 0.94
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 Q8ZH62
- Elsewhere: RCSB PDB 5DUL · PDBe 5DUL · UniProt Q8ZH62
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