Research workbench
Nitrogenase MoFeP protein in the IDS oxidized state
Analyse Nitrogenase MoFeP protein in the IDS oxidized state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOJ
- Type
- protein
- Length
- 1,981 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.592
- Source
- Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5)
- Molecule
- Nitrogenase protein alpha chain; Nitrogenase FeMo beta subunit protein NifK
- EC
- 1.18.6.1
- UniProt
- A9H5W5, A9H5W8
- Ligands
- HCA, ICS, CLF, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.592 · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase protein alpha chain (EC 1.18.6.1) | protein | 481 | 47% helix, 15% strand | A9H5W5 |
| B, D | Nitrogenase FeMo beta subunit protein NifK (EC 1.18.6.1) | protein | 510 | 50% helix, 13% strand | A9H5W8 |
| C | Nitrogenase protein alpha chain (EC 1.18.6.1) | protein | 480 | 46% helix, 15% strand | A9H5W5 |
Ligands and binding sites
- HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, C, D
- ICS · iron-sulfur-molybdenum cluster with interstitial carbon · ligand · 2 copies · chains A, C
- CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, C, D
- FE · Fe (III) 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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.88 | 0.95 | 76 | HCA, ICS |
| 2 | 492 | 0.87 | 0.94 | 70 | HCA, ICS |
| 3 | 454 | 0.85 | 0.93 | 36 | empty |
| 4 | 79 | 0.75 | 0.98 | 18 | empty |
| 5 | 75 | 0.73 | 0.97 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4702 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4653 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 2953 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 1313 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1308 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5KOJ · Nitrogenase mofep protein in the ids oxidized state · 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
- Every structure of UniProt A9H5W5
- Every structure of UniProt A9H5W8
- Elsewhere: RCSB PDB 5KOJ · PDBe 5KOJ · UniProt A9H5W5 · UniProt A9H5W8
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