MolNFT v1 · #168845 · protein
Crystal structure of putative NAD(P)H-flavin oxidoreductase from neisseria meningitidis
6WT2: “Crystal structure of putative NAD(P)H-flavin oxidoreductase from neisseria meningitidis”. X-ray diffraction, 3 ligands (NIO, FMN, CL), 9 pockets (best druggability 0.76). MolNFT v1 #168845 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WT2
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD(P)H-flavin oxidoreductase
- UniProt
- A0A0U1RIB4
- Ligands
- NIO, FMN, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative NAD(P)H-flavin oxidoreductase | protein | 221 | 48% helix, 15% strand | A0A0U1RIB4 |
Ligands and binding sites
- NIO · Nicotinic acid · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
- FMT · Formic acid · additive · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.76 | 0.81 | 85 | NIO, FMT, FMN |
| 2 | 432 | 0.74 | 0.84 | 55 | FMN, NIO |
| 3 | 362 | 0.74 | 0.85 | 42 | EDO, FMN, NIO |
| 4 | 407 | 0.73 | 0.83 | 48 | NIO, EDO, FMN |
| 5 | 112 | 0.47 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4286 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 4222 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 127 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 6WT2 · Crystal Structure of Putative NAD(P)H-Flavin Oxidoreductase from Neisseria meningitidis · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0U1RIB4
- Elsewhere: RCSB PDB 6WT2 · PDBe 6WT2 · UniProt A0A0U1RIB4
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