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Cryoem structure of azotobacter vinelandii nitrogenase mofep during catalytic N2 reduction
Analyse Cryoem structure of azotobacter vinelandii nitrogenase mofep during catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DPN
- Type
- protein
- Length
- 1,998 residues
- Chains
- 4
- Method
- electron microscopy
- 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, C1DGZ8
- Ligands
- HCA, ICS, CLF, FE
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 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 | 48% helix, 14% strand | P07328 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 522 | 51% helix, 10% strand | C1DGZ8 |
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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.88 | 0.94 | 75 | HCA, ICS |
| 2 | 463 | 0.86 | 0.94 | 51 | HCA, ICS |
| 3 | 859 | 0.85 | 0.87 | 64 | empty |
| 4 | 102 | 0.78 | 0.98 | 34 | empty |
| 5 | 643 | 0.75 | 0.81 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4696 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 4673 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 3099 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 1398 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1383 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 8DPN · CryoEM structure of Azotobacter vinelandii nitrogenase MoFeP during catalytic N2 reduction · the same entry in another collection · chain B against B, 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
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 C1DGZ8
- Elsewhere: RCSB PDB 8DPN · PDBe 8DPN · UniProt P07328 · UniProt C1DGZ8
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