MolNFT v1 · #19328 · protein
Nitrogenase mofe protein from klebsiella pneumoniae, as-crystallized (mixed oxidation) state
1QH8 · Protein (nitrogenase molybdenum iron protein): “Nitrogenase mofe protein from klebsiella pneumoniae, as-crystallized (mixed oxidation) state”. X-ray diffraction, 5 ligands (HCA, CFM, CLF), 20 pockets (best druggability 0.88). MolNFT…
- PDB
- 1QH8
- Type
- protein
- Length
- 1,994 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (nitrogenase molybdenum iron protein)
- EC
- 1.18.6.1
- UniProt
- P00466, P09772
- Ligands
- HCA, CFM, CLF, MG, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (nitrogenase molybdenum iron protein) (EC 1.18.6.1) | protein | 478 | 47% helix, 15% strand | P00466 |
| B, D | Protein (nitrogenase molybdenum iron protein) (EC 1.18.6.1) | protein | 519 | 50% helix, 12% strand | P09772 |
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
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.88 | 0.94 | 80 | HCA, CFM |
| 2 | 479 | 0.87 | 0.94 | 65 | HCA, CFM |
| 3 | 1065 | 0.86 | 0.87 | 71 | EDO |
| 4 | 89 | 0.77 | 0.98 | 29 | empty |
| 5 | 97 | 0.76 | 0.97 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4610 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4578 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 2770 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1287 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1275 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1QH8 · Nitrogenase mofe protein from klebsiella pneumoniae, as-crystallized (mixed oxidation)… · the same entry in another collection · chain A against A, TM-score 1.00
- P00466 · 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 1.00
- P09772 · 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 P00466
- Every structure of UniProt P09772
- Elsewhere: RCSB PDB 1QH8 · PDBe 1QH8 · UniProt P00466 · UniProt P09772
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