MolNFT v1 · #107867 · protein
Structure of the unready ni-a state of the S499C mutant of D. fructosovorans nife-hydrogenase
4UPE · Nife-hydrogenase small subunit: “Structure of the unready ni-a state of the S499C mutant of D. fructosovorans nife-hydrogenase”. X-ray diffraction, 6 ligands (SF4, F3S, FCO), 19 pockets (best druggability 0.80). MolNFT v1 #107867 on…
- PDB
- 4UPE
- Type
- protein
- Length
- 2,418 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nife-hydrogenase small subunit; Nickel-dependent hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- P18187, P18188
- Ligands
- SF4, F3S, FCO, CA, NI, PO4
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nife-hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | P18187 |
| C | Nife-hydrogenase small subunit (EC 1.12.2.1) | protein | 261 | 36% helix, 17% strand | P18187 |
| Q | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 48% helix, 15% strand | P18188 |
| R, S | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 16% strand | P18188 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, Q, B, R, C, S
- F3S · FE3-S4 cluster · ligand · 3 copies · chains A, Q, B, R, C, S
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 3 copies · chains Q, R, S
- CA · Calcium ion · metal · 4 copies · chains Q, R, S
- NI · Nickel (II) ion · metal · 3 copies · chains Q, R, S
- PO4 · Phosphate ion · ion · 2 copies · chains Q, C, R
- GOL · Glycerol · additive · 5 copies · chains Q, A, C, R, B, S
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.80 | 0.82 | 86 | empty |
| 2 | 688 | 0.79 | 0.83 | 97 | GOL |
| 3 | 102 | 0.76 | 0.96 | 38 | empty |
| 4 | 93 | 0.76 | 0.96 | 29 | empty |
| 5 | 57 | 0.72 | 0.98 | 26 | empty |
Interfaces
8 interfaces between chains.
- C–S · 3604 Ų buried · 58 hydrogen bonds · protein-protein
- A–Q · 3602 Ų buried · 54 hydrogen bonds · protein-protein
- B–R · 3582 Ų buried · 55 hydrogen bonds · protein-protein
- C–R · 595 Ų buried · 10 hydrogen bonds · protein-protein
- C–Q · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, oxidation).
Compared structures
- 4UPE · Structure of the unready Ni-A state of the S499C mutant of D. fructosovorans… · the same entry in another collection · chain S against S, TM-score 1.00
- P18188 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain Q against A, TM-score 1.00
- P18187 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain C 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 P18187
- Every structure of UniProt P18188
- Elsewhere: RCSB PDB 4UPE · PDBe 4UPE · UniProt P18187 · UniProt P18188
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