Research workbench
Structure of the nitrogenase mofe protein from clostridium pasteurianum pressurized with xenon
Analyse Structure of the nitrogenase mofe protein from clostridium pasteurianum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WN9
- Type
- protein
- Length
- 1,950 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, PRO, FE, XE
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 517 | 46% helix, 13% strand | P00467 |
| B, D | Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1) | protein | 458 | 48% helix, 14% strand | P11347 |
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
- PRO · Proline · ligand · 2 copies · chains B, D
- FE · Fe (III) ion · metal · 2 copies · chains B, D
- XE · Xenon · ion · 6 copies · chains A, B, C, D
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 | 1013 | 0.89 | 0.91 | 115 | PRO |
| 2 | 585 | 0.88 | 0.94 | 77 | HCA, ICS |
| 3 | 604 | 0.88 | 0.93 | 85 | HCA, ICS |
| 4 | 660 | 0.74 | 0.80 | 52 | empty |
| 5 | 50 | 0.70 | 0.98 | 24 | CLF |
Interfaces
5 interfaces between chains.
- A–B · 3371 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3351 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 2463 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 1235 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4WN9 · Structure of the Nitrogenase MoFe Protein from Clostridium pasteurianum Pressurized with… · the same entry in another collection · chain D against D, 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 C 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 4WN9 · PDBe 4WN9 · UniProt P00467 · UniProt P11347
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.