Research workbench
Nitrogenase mofep from gluconacetobacter diazotrophicus in dithionite reduced state
Analyse Nitrogenase mofep from gluconacetobacter diazotrophicus in dithionite reduced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOH
- Type
- protein
- Length
- 1,985 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogenase protein alpha chain; Nitrogenase femo beta subunit protein nifk
- EC
- 1.18.6.1
- UniProt
- A9H5W5, A9H5W8
- Ligands
- HCA, ICS, CLF, FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogenase protein alpha chain (EC 1.18.6.1) | protein | 483 | 47% helix, 15% strand | A9H5W5 |
| B, D | Nitrogenase femo beta subunit protein nifk (EC 1.18.6.1) | protein | 510 | 51% helix, 13% strand | A9H5W8 |
| C | Nitrogenase protein alpha chain (EC 1.18.6.1) | protein | 482 | 48% helix, 15% strand | A9H5W5 |
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 B, C, D, A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.88 | 0.95 | 74 | HCA, ICS |
| 2 | 469 | 0.87 | 0.94 | 64 | HCA, ICS |
| 3 | 548 | 0.86 | 0.92 | 52 | empty |
| 4 | 81 | 0.75 | 0.97 | 19 | MRD |
| 5 | 60 | 0.74 | 0.99 | 23 | CLF |
Interfaces
5 interfaces between chains.
- C–D · 4678 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 4662 Ų buried · 58 hydrogen bonds · protein-protein
- B–D · 2921 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 1307 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1297 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5KOH · Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state · the same entry in another collection · chain B against B, 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 A9H5W5
- Every structure of UniProt A9H5W8
- Elsewhere: RCSB PDB 5KOH · PDBe 5KOH · UniProt A9H5W5 · UniProt A9H5W8
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