MolNFT v1 · #137479 · protein
Nitrogenase CP1 at pH 5
5VPW · Nitrogenase molybdenum-iron protein alpha chain: “Nitrogenase CP1 at pH 5”. X-ray diffraction, 4 ligands (HCA, ICS, CLF), 20 pockets (best druggability 0.89). MolNFT v1 #137479 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VPW
- Type
- protein
- Length
- 1,928 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
- P00467, P11347
- Ligands
- HCA, ICS, CLF, FE2
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 517 | 44% helix, 13% strand | P00467 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 458 | 49% helix, 14% strand | P11347 |
| C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 495 | 44% helix, 14% strand | P00467 |
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
- FE2 · Fe (II) 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.89 | 0.90 | 110 | empty |
| 2 | 654 | 0.89 | 0.93 | 81 | HCA, ICS |
| 3 | 649 | 0.88 | 0.93 | 88 | HCA, ICS |
| 4 | 817 | 0.79 | 0.82 | 80 | empty |
| 5 | 60 | 0.74 | 0.99 | 23 | CLF |
Interfaces
5 interfaces between chains.
- A–B · 3412 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3327 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2401 Ų buried · 63 hydrogen bonds · protein-protein
- A–D · 1247 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1235 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5VPW · Nitrogenase Cp1 at pH 5 · the same entry in another collection · chain A against A, TM-score 1.00
- P11347 · 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 0.99
- P00467 · 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 0.99
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 P00467
- Every structure of UniProt P11347
- Elsewhere: RCSB PDB 5VPW · PDBe 5VPW · UniProt P00467 · UniProt P11347
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