MolNFT v1 · #14717 · protein
X-ray crystal structure of the nitrogenase molybdenum-iron protein from clostridium pasteurianum at 3.0 ångströms resolution
1MIO · Nitrogenase molybdenum iron protein (alpha chain): “X-ray crystal structure of the nitrogenase molybdenum-iron protein from clostridium pasteurianum at 3.0…”. X-ray diffraction, 4 ligands (HCA, CFM, CLP), 20 pockets (best…
- PDB
- 1MIO
- Type
- protein
- Length
- 1,964 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…
- UniProt
- P00467, P11347
- Ligands
- HCA, CFM, CLP, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum iron protein (alpha chain) | protein | 525 | 45% helix, 15% strand | P00467 |
| B, D | Nitrogenase molybdenum iron protein (beta chain) | protein | 457 | 46% helix, 15% strand | P11347 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, 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, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.88 | 0.94 | 74 | HCA, CFM |
| 2 | 592 | 0.88 | 0.94 | 74 | HCA, CFM |
| 3 | 852 | 0.87 | 0.89 | 58 | empty |
| 4 | 135 | 0.79 | 0.96 | 29 | empty |
| 5 | 111 | 0.77 | 0.96 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3304 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3300 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 2486 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 1337 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1224 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1MIO · X-ray crystal structure of the nitrogenase molybdenum-iron protein from clostridium… · the same entry in another collection · chain C against C, TM-score 1.00
- P11347 · 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 0.99
- P00467 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein alpha chain… · a predicted model of the same protein · chain A 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 P00467
- Every structure of UniProt P11347
- Elsewhere: RCSB PDB 1MIO · PDBe 1MIO · UniProt P00467 · UniProt P11347
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