Research workbench
Nitrogenase molybdenum-iron protein from clostridium pasteurianum at 1.08 a resolution
Analyse Nitrogenase molybdenum-iron protein from clostridium pasteurianum at 1.08 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WES
- Type
- protein
- Length
- 1,953 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 0.88
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1) | protein | 519 | 46% 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 | 518 | 46% helix, 13% 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
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.88 | 0.90 | 86 | empty |
| 2 | 610 | 0.88 | 0.93 | 90 | HCA, ICS |
| 3 | 554 | 0.87 | 0.93 | 81 | HCA, ICS |
| 4 | 577 | 0.74 | 0.82 | 44 | empty |
| 5 | 51 | 0.70 | 0.98 | 20 | CLF |
Interfaces
5 interfaces between chains.
- A–B · 3347 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 3342 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2487 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 1232 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1213 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4WES · Nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution · 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 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 4WES · PDBe 4WES · UniProt P00467 · UniProt P11347
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