MolNFT v1 · #107884 · protein
Low X-ray dose structure of a ni-a ni-sox mixture of the D. fructosovorans nife-hydrogenase L122A mutant
4UPV · Nife-hydrogenase small subunit: “Low X-ray dose structure of a ni-a ni-sox mixture of the D. fructosovorans nife-hydrogenase L122A mutant”. X-ray diffraction, 9 ligands (SF4, F3S, GLY), 10 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4UPV
- Type
- protein
- Length
- 1,614 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nife-hydrogenase small subunit; Nife-hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- E1K248, E1K247
- Ligands
- SF4, F3S, GLY, FCO, SOT, NI, MG, H2S, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nife-hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | E1K248 |
| B | Nife-hydrogenase small subunit (EC 1.12.2.1) | protein | 263 | 37% helix, 17% strand | E1K248 |
| Q | Nife-hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 15% strand | E1K247 |
| R | Nife-hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 49% helix, 15% strand | E1K247 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, Q, B, R
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, Q, B, R
- GLY · Glycine · ligand · 2 copies · chains B, R
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains Q, R
- SOT · morpholine-4-sulfonic acid · ligand · chains B
- NI · Nickel (II) ion · metal · 2 copies · chains Q, R
- MG · Magnesium ion · metal · 2 copies · chains Q, R
- H2S · Hydrosulfuric acid · ion · chains B, R
- CL · Chloride ion · ion · chains Q
- GOL · Glycerol · additive · 14 copies · chains A, Q, B, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.81 | 0.97 | 47 | empty |
| 2 | 161 | 0.81 | 0.96 | 44 | GLY |
| 3 | 712 | 0.74 | 0.80 | 51 | empty |
| 4 | 288 | 0.55 | 0.76 | 34 | empty |
| 5 | 99 | 0.46 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–Q · 3559 Ų buried · 58 hydrogen bonds · protein-protein
- B–R · 3552 Ų buried · 58 hydrogen bonds · protein-protein
- Q–R · 273 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide, 1 covalent (oxidation, disulfide, covalent ligand).
Compared structures
- 4UPV · Low X-ray dose structure of a Ni-A Ni-Sox mixture of the D. fructosovorans… · the same entry in another collection · chain A against A, 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 E1K248
- Every structure of UniProt E1K247
- Elsewhere: RCSB PDB 4UPV · PDBe 4UPV · UniProt E1K248 · UniProt E1K247
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