Research workbench
Wild type fe-type nitrile hydratase from comamonas testosteroni NI1
Analyse Wild type fe-type nitrile hydratase from comamonas testosteroni NI1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FM4
- Type
- protein
- Length
- 3,296 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrile hydratase alpha subunit; Nitrile hydratase beta subunit
- EC
- 4.2.1.84
- Ligands
- FE, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Nitrile hydratase alpha subunit (EC 4.2.1.84) | protein | 206 | 43% helix, 12% strand | — |
| B, D, F, H, J, L, N, P | Nitrile hydratase beta subunit (EC 4.2.1.84) | protein | 206 | 33% helix, 16% strand | — |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, C, E, G, I, K, M, O
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, E, F, G, H, I, J, K, M, N, O, P
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 | 953 | 0.85 | 0.87 | 111 | PO4 |
| 2 | 298 | 0.80 | 0.92 | 32 | empty |
| 3 | 304 | 0.80 | 0.91 | 37 | empty |
| 4 | 297 | 0.80 | 0.91 | 36 | empty |
| 5 | 312 | 0.76 | 0.88 | 41 | PO4 |
Interfaces
29 interfaces between chains.
- C–D · 3261 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3256 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 3254 Ų buried · 48 hydrogen bonds · protein-protein
- G–H · 3244 Ų buried · 48 hydrogen bonds · protein-protein
- O–P · 3243 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (oxidation).
Compared structures
- 4FM4 · Wild Type Fe-type Nitrile Hydratase from Comamonas testosteroni Ni1 · 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
- Elsewhere: RCSB PDB 4FM4 · PDBe 4FM4
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