Research workbench
Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from nitrosomonas europaea
Analyse Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FAS
- Type
- protein
- Length
- 1,653 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxylamine oxidoreductase; NE1300
- EC
- 1.7.3.4
- UniProt
- Q50925, Q82V11
- Ligands
- HEC, ISW, NO3
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hydroxylamine oxidoreductase (EC 1.7.3.4) | protein | 502 | 51% helix, 2% strand | Q50925 |
| D, E, F | NE1300 | protein | 49 | 33% helix, 31% strand | Q82V11 |
Ligands and binding sites
- HEC · Heme C · ligand · 21 copies · chains A, C, B
- ISW · {3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~n~21~,n~22~,n~23~, n~24~]dipropanoato(2-)}iron · ligand · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 4 copies · chains B, C, F
- PEG · Di(hydroxyethyl)ether · additive · 17 copies · chains A, B, C, F
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- P6G · Hexaethylene glycol · additive · chains B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.86 | 0.95 | 62 | HEC |
| 2 | 331 | 0.86 | 0.95 | 57 | HEC |
| 3 | 797 | 0.84 | 0.87 | 66 | PEG |
| 4 | 283 | 0.84 | 0.95 | 53 | HEC |
| 5 | 226 | 0.83 | 0.95 | 46 | HEC |
Interfaces
9 interfaces between chains.
- A–B · 2812 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2806 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2798 Ų buried · 41 hydrogen bonds · protein-protein
- C–F · 623 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 cofactor, 9 covalent, 3 disulfide (heme c attachment, covalent ligand, disulfide).
Compared structures
- 4FAS · Complex crystal structure of hydroxylamine oxidoreductase and NE1300 from Nitrosomonas… · the same entry in another collection · chain C against C, TM-score 1.00
- Q50925 · AlphaFold monomer V2.0 prediction for hydroxylamine oxidoreductase (Q50925) · a predicted model of the same protein · 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 Q50925
- Every structure of UniProt Q82V11
- Elsewhere: RCSB PDB 4FAS · PDBe 4FAS · UniProt Q50925 · UniProt Q82V11
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