MolNFT v1 · #140249 · protein
Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris miyazaki F [nife]-hydrogenase
5Y4N · Periplasmic [nife] hydrogenase small subunit: “Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris miyazaki F…”. X-ray diffraction, 4 ligands (SF4, F3S, NFU), 9 pockets (best druggability 0.74).…
- PDB
- 5Y4N
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nife] hydrogenase small subunit; Periplasmic [nife] hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- P21853, P21852
- Ligands
- SF4, F3S, NFU, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 264 | 38% helix, 16% strand | P21853 |
| L | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 534 | 48% helix, 16% strand | P21852 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains S, L
- F3S · FE3-S4 cluster · ligand · chains S, L
- NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · chains L
- MG · Magnesium ion · metal · chains L
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains S, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains S
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.74 | 0.96 | 22 | empty |
| 2 | 52 | 0.72 | 0.98 | 21 | empty |
| 3 | 92 | 0.52 | 0.83 | 20 | empty |
| 4 | 79 | 0.48 | 0.82 | 22 | empty |
| 5 | 64 | 0.43 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- S–L · 3703 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5Y4N · Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris… · the same entry in another collection · chain S against S, TM-score 1.00
- P21852 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain L against A, TM-score 1.00
- P21853 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain S 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 P21853
- Every structure of UniProt P21852
- Elsewhere: RCSB PDB 5Y4N · PDBe 5Y4N · UniProt P21853 · UniProt P21852
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