MolNFT v1 · #137487 · protein
Nitrogenase AV1 at pH 5
5VQ4 · Nitrogenase molybdenum-iron protein alpha chain: “Nitrogenase AV1 at pH 5”. X-ray diffraction, 4 ligands (HCA, ICS, CLF), 20 pockets (best druggability 0.88). MolNFT v1 #137487 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VQ4
- 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, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 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
- FE · Fe (III) ion · metal · 2 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.88 | 0.94 | 75 | HCA, ICS |
| 2 | 427 | 0.86 | 0.94 | 50 | HCA, ICS |
| 3 | 1189 | 0.85 | 0.86 | 85 | empty |
| 4 | 94 | 0.78 | 0.98 | 29 | empty |
| 5 | 96 | 0.77 | 0.98 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4766 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 4763 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 3168 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 1389 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1383 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5VQ4 · Nitrogenase Av1 at pH 5 · the same entry in another collection · chain D against D, 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 5VQ4 · PDBe 5VQ4 · UniProt P07328 · UniProt P07329
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