Research workbench
Selenium incorporated femo-cofactor of nitrogenase from azotobacter vinelandii with low concentration of selenium
Analyse Selenium incorporated femo-cofactor of nitrogenase from azotobacter vinelandii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OP3
- Type
- protein
- Length
- 1,998 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, ICS, CLF, CA, MG, SE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 477 | 47% helix, 14% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 53% helix, 11% strand | P07329 |
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
- CA · Calcium ion · metal · 4 copies · chains B, C, D, A
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SE · Selenium atom · ion · 2 copies · chains A, C
- IMD · Imidazole · additive · 12 copies · chains A, D, B, 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 | 554 | 0.88 | 0.94 | 75 | HCA, ICS, SE, IMD |
| 2 | 453 | 0.87 | 0.94 | 54 | HCA, ICS, SE |
| 3 | 1139 | 0.85 | 0.86 | 78 | IMD |
| 4 | 97 | 0.77 | 0.98 | 30 | empty |
| 5 | 93 | 0.77 | 0.98 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 4729 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 4719 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 3133 Ų buried · 58 hydrogen bonds · protein-protein
- A–D · 1380 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1371 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6OP3 · Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low… · 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 A 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 6OP3 · PDBe 6OP3 · UniProt P07328 · UniProt P07329
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