Research workbench
Crystal structure of the alpha-H195Q mutant of nitrogenase
Analyse Crystal structure of the alpha-H195Q mutant of nitrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FP4
- Type
- protein
- Length
- 1,979 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase molybdenum-iron protein alpha chain; Nitrogenase molybdenum-iron protein beta…
- EC
- 1.18.6.1
- UniProt
- P07328, P07329
- Ligands
- HCA, CFM, CLP, CA
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 467 | 50% helix, 15% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 53% helix, 11% strand | P07329 |
| C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 468 | 49% helix, 15% strand | P07328 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, C, D
- CFM · Fe-Mo-S cluster · ligand · 2 copies · chains A, C
- CLP · Fe-S cluster · ligand · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.88 | 0.94 | 77 | HCA, CFM |
| 2 | 508 | 0.88 | 0.94 | 78 | HCA, CFM |
| 3 | 1177 | 0.85 | 0.86 | 79 | empty |
| 4 | 93 | 0.77 | 0.98 | 28 | empty |
| 5 | 89 | 0.75 | 0.97 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4706 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 4694 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 3111 Ų buried · 56 hydrogen bonds · protein-protein
- A–D · 1367 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1352 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1FP4 · Crystal structure of the alpha-H195Q mutant of nitrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- P07328 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein alpha chain… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P07329 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein beta chain… · a predicted model of the same protein · chain B 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 P07328
- Every structure of UniProt P07329
- Elsewhere: RCSB PDB 1FP4 · PDBe 1FP4 · UniProt P07328 · UniProt P07329
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