MolNFT v1 · #185660 · protein
Structure of wrba from yersinia pseudotuberculosis in P1
7Q6M · NAD(P)H dehydrogenase (quinone): “Structure of wrba from yersinia pseudotuberculosis in P1”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.82). MolNFT v1 #185660 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7Q6M
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase (quinone)
- EC
- 1.6.5.2
- UniProt
- Q66BP3
- Ligands
- CL
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 198 | 39% helix, 21% strand | Q66BP3 |
| B, D | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 206 | 38% helix, 20% strand | Q66BP3 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.82 | 0.98 | 24 | empty |
| 2 | 145 | 0.80 | 0.97 | 34 | empty |
| 3 | 142 | 0.79 | 0.96 | 33 | empty |
| 4 | 450 | 0.69 | 0.80 | 39 | CL |
| 5 | 379 | 0.68 | 0.81 | 39 | CL |
Interfaces
6 interfaces between chains.
- A–D · 1077 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1076 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 874 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 756 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
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 Q66BP3
- Elsewhere: RCSB PDB 7Q6M · PDBe 7Q6M · UniProt Q66BP3
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