MolNFT v1 · #107533 · protein
Structure of anaerobically purified D. fructosovorans nife- hydrogenase
4UD2 · Hydrogenase (nife) small subunit hyda: “Structure of anaerobically purified D. fructosovorans nife- hydrogenase”. X-ray diffraction, 5 ligands (SF4, F3S, FCO), 15 pockets (best druggability 0.82). MolNFT v1 #107533 on GenesisL1: 3D…
- PDB
- 4UD2
- Type
- protein
- Length
- 2,416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase (nife) small subunit hyda; Nickel-dependent hydrogenase large subunit
- EC
- 1.12.2.1
- UniProt
- E1K248, E1K247
- Ligands
- SF4, F3S, FCO, NI, MG
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | E1K248 |
| C | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 260 | 38% helix, 17% strand | E1K248 |
| Q, R, S | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 16% strand | E1K247 |
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
- NI · Nickel (II) ion · metal · 3 copies · chains Q, R, S
- MG · Magnesium ion · metal · 3 copies · chains Q, R, S
- GOL · Glycerol · additive · 14 copies · chains A, Q, B, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.82 | 0.96 | 54 | empty |
| 2 | 152 | 0.81 | 0.97 | 52 | empty |
| 3 | 111 | 0.77 | 0.96 | 43 | empty |
| 4 | 831 | 0.69 | 0.75 | 58 | empty |
| 5 | 52 | 0.62 | 0.94 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–R · 3606 Ų buried · 56 hydrogen bonds · protein-protein
- A–Q · 3595 Ų buried · 56 hydrogen bonds · protein-protein
- C–S · 3595 Ų buried · 59 hydrogen bonds · protein-protein
- B–S · 100 Ų buried · 0 hydrogen bonds · protein-protein
- R–S · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, oxidation).
Compared structures
- 4UD2 · Structure of anaerobically purified D. fructosovorans NiFe- hydrogenase · the same entry in another collection · chain C against C, 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 4UD2 · PDBe 4UD2 · UniProt E1K248 · UniProt E1K247
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