MolNFT v1 · #49105 · protein
Crystal structure of fe-type nhase from rhodococcus erythropolis AJ270
2QDY · Nitrile hydratase subunit alpha: “Crystal structure of fe-type nhase from rhodococcus erythropolis AJ270”. X-ray diffraction, 4 ligands (IBN, MG, FE), 3 pockets (best druggability 0.51). MolNFT v1 #49105 on GenesisL1: 3D structure…
- PDB
- 2QDY
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrile hydratase subunit alpha; Nitrile hydratase subunit beta
- EC
- 4.2.1.84
- UniProt
- P13448, P13449
- Ligands
- IBN, MG, FE, CL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrile hydratase subunit alpha (EC 4.2.1.84) | protein | 197 | 45% helix, 13% strand | P13448 |
| B | Nitrile hydratase subunit beta (EC 4.2.1.84) | protein | 211 | 31% helix, 14% strand | P13449 |
Ligands and binding sites
- IBN · 2-methylpropan-1-amine · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- FE · Fe (III) ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.51 | 0.77 | 39 | empty |
| 2 | 94 | 0.43 | 0.79 | 24 | empty |
| 3 | 104 | 0.38 | 0.75 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 3773 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2QDY · Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270 · the same entry in another collection · chain A 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 A against A, 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 0.99
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 2QDY · PDBe 2QDY · UniProt P13448 · UniProt P13449
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