MolNFT v1 · #107536 · protein
Structure of methylviologen-treated anaerobically purified D. fructosovorans nife-hydrogenase
4UD6 · Hydrogenase (nife) small subunit hyda: “Structure of methylviologen-treated anaerobically purified D. fructosovorans nife-hydrogenase”. X-ray diffraction, 5 ligands (SF4, F3S, FCO), 19 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 4UD6
- Type
- protein
- Length
- 2,417 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
- 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 | 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 | 36% helix, 17% strand | E1K248 |
| Q, S | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 48% helix, 17% strand | E1K247 |
| R | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 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 · 15 copies · chains A, Q, C, R, B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.80 | 0.82 | 77 | empty |
| 2 | 101 | 0.77 | 0.96 | 33 | empty |
| 3 | 82 | 0.75 | 0.96 | 26 | empty |
| 4 | 66 | 0.74 | 0.98 | 25 | empty |
| 5 | 390 | 0.71 | 0.83 | 46 | GOL |
Interfaces
8 interfaces between chains.
- B–R · 3607 Ų buried · 53 hydrogen bonds · protein-protein
- A–Q · 3586 Ų buried · 57 hydrogen bonds · protein-protein
- C–S · 3565 Ų buried · 55 hydrogen bonds · protein-protein
- C–R · 552 Ų buried · 7 hydrogen bonds · protein-protein
- C–Q · 456 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, oxidation).
Compared structures
- 4UD6 · Structure of methylviologen-treated anaerobically purified D. fructosovorans… · 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 4UD6 · PDBe 4UD6 · UniProt E1K248 · UniProt E1K247
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