Research workbench
Crystal structure of the nitrogenase fe protein PHE135TRP with mgadp bound
Analyse Crystal structure of the nitrogenase fe protein PHE135TRP with mgadp bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XCP
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase iron protein 1
- EC
- 1.18.6.1
- UniProt
- P00459
- Ligands
- ADP, SF4, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nitrogenase iron protein 1 (EC 1.18.6.1) | protein | 289 | 36% helix, 14% strand | P00459 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.80 | 0.82 | 120 | MG, ADP |
| 2 | 716 | 0.73 | 0.79 | 78 | MG, ADP |
| 3 | 705 | 0.73 | 0.79 | 76 | MG, ADP |
| 4 | 77 | 0.60 | 0.89 | 17 | empty |
| 5 | 85 | 0.40 | 0.78 | 21 | SF4 |
Interfaces
2 interfaces between chains.
- A–B · 1898 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1826 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1XCP · Crystal Structure of the Nitrogenase Fe protein Phe135Trp with MgADP bound · the same entry in another collection · chain A against A, TM-score 1.00
- P00459 · AlphaFold monomer V2.0 prediction for nitrogenase iron protein 1 (P00459) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P00459
- Elsewhere: RCSB PDB 1XCP · PDBe 1XCP · UniProt P00459
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