MolNFT v1 · #31034 · protein
Nitrile hydratase complexed with nitric oxide
2AHJ: “Nitrile hydratase complexed with nitric oxide”. X-ray diffraction, 4 ligands (FE, ZN, SO4), 13 pockets (best druggability 0.83). MolNFT v1 #31034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2AHJ
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrile hydratase
- EC
- 4.2.1.84
- UniProt
- P13448, P13449
- Ligands
- FE, ZN, SO4, NO
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrile hydratase (EC 4.2.1.84) | protein | 194 | 44% helix, 13% strand | P13448 |
| B | Nitrile hydratase (EC 4.2.1.84) | protein | 211 | 31% helix, 14% strand | P13449 |
| C | Nitrile hydratase (EC 4.2.1.84) | protein | 195 | 46% helix, 13% strand | P13448 |
| D | Nitrile hydratase (EC 4.2.1.84) | protein | 212 | 31% helix, 14% strand | P13449 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- NO · Nitric oxide · ion · 2 copies · chains A, B, C, D
- DIO · 1,4-diethylene dioxide · additive · 2 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 | 456 | 0.83 | 0.90 | 40 | empty |
| 2 | 56 | 0.68 | 0.96 | 14 | NO, DIO |
| 3 | 60 | 0.67 | 0.95 | 14 | NO, DIO |
| 4 | 75 | 0.56 | 0.87 | 25 | empty |
| 5 | 88 | 0.53 | 0.85 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3783 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3713 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 1183 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 388 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2AHJ · Nitrile hydratase complexed with nitric oxide · the same entry in another collection · chain D against D, TM-score 1.00
- P13449 · AlphaFold monomer V2.0 prediction for nitrile hydratase subunit beta (P13449) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P13448 · AlphaFold monomer V2.0 prediction for nitrile hydratase subunit alpha (P13448) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P13448
- Every structure of UniProt P13449
- Elsewhere: RCSB PDB 2AHJ · PDBe 2AHJ · UniProt P13448 · UniProt P13449
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.