MolNFT v1 · #118515 · protein
Structure of B. abortus wrba-related protein a (wrpa)
5F4B · NAD(P)H dehydrogenase (quinone): “Structure of B. abortus wrba-related protein a (wrpa)”. X-ray diffraction, 2 ligands (FMN, CL), 4 pockets (best druggability 0.51). MolNFT v1 #118515 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F4B
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase (quinone)
- EC
- 1.6.5.2
- UniProt
- Q2YQ23
- Ligands
- FMN, CL
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 173 | 47% helix, 20% strand | Q2YQ23 |
| B | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 172 | 47% helix, 20% strand | Q2YQ23 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.51 | 0.86 | 16 | FMN |
| 2 | 61 | 0.50 | 0.85 | 16 | FMN |
| 3 | 147 | 0.43 | 0.75 | 21 | empty |
| 4 | 80 | 0.36 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 6 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 Q2YQ23
- Elsewhere: RCSB PDB 5F4B · PDBe 5F4B · UniProt Q2YQ23
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