MolNFT v1 · #38836 · protein
The crystal structure of the putative NAD(P)H-flavin oxidoreductase from streptococcus pyogenes M1 gas
2HAY: “The crystal structure of the putative NAD(P)H-flavin oxidoreductase from streptococcus pyogenes M1 gas”. X-ray diffraction, 2 ligands (FMN, SO4), 13 pockets (best druggability 0.77). MolNFT v1 #38836 on GenesisL1: 3D structure…
- PDB
- 2HAY
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD(P)H-flavin oxidoreductase
- EC
- 1.-.-.-
- UniProt
- Q9A120
- Ligands
- FMN, SO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NAD(P)H-flavin oxidoreductase (EC 1.-.-.-) | protein | 217 | 47% helix, 17% strand | Q9A120 |
| B | Putative NAD(P)H-flavin oxidoreductase (EC 1.-.-.-) | protein | 221 | 48% helix, 16% strand | Q9A120 |
| C | Putative NAD(P)H-flavin oxidoreductase (EC 1.-.-.-) | protein | 216 | 49% helix, 17% strand | Q9A120 |
| D | Putative NAD(P)H-flavin oxidoreductase (EC 1.-.-.-) | protein | 222 | 48% helix, 16% strand | Q9A120 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.77 | 0.79 | 93 | FMN |
| 2 | 524 | 0.76 | 0.84 | 47 | FMN, SO4 |
| 3 | 105 | 0.73 | 0.95 | 19 | empty |
| 4 | 430 | 0.71 | 0.82 | 46 | FMN |
| 5 | 611 | 0.71 | 0.79 | 47 | SO4, FMN |
Interfaces
6 interfaces between chains.
- A–B · 3883 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3860 Ų buried · 60 hydrogen bonds · protein-protein
- B–D · 541 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 87 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2HAY · The Crystal Structure of the Putative NAD(P)H-Flavin Oxidoreductase from Streptococcus… · 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 Q9A120
- Elsewhere: RCSB PDB 2HAY · PDBe 2HAY · UniProt Q9A120
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