MolNFT v1 · #107585 · protein
Structure of the V74C large subunit mutant of D. fructosovorans nife- hydrogenase
4UEQ · Hydrogenase (nife) small subunit hyda: “Structure of the V74C large subunit mutant of D. fructosovorans nife- hydrogenase”. X-ray diffraction, 8 ligands (SF4, F3S, FCO), 20 pockets (best druggability 0.81). MolNFT v1 #107585 on…
- PDB
- 4UEQ
- Type
- protein
- Length
- 4,836 residues
- Chains
- 12
- 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, MG, NI, CA, H2S, CO3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | E1K248 |
| C, F | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 261 | 37% helix, 16% strand | E1K248 |
| Q, S, T, V | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 15% strand | E1K247 |
| R, U | 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 · 12 copies · chains A, Q, B, R, C, S, D, T, E, U, F, V
- F3S · FE3-S4 cluster · ligand · 6 copies · chains A, Q, B, R, C, S, D, T, E, U, F, V
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 6 copies · chains Q, R, S, T, U, V
- MG · Magnesium ion · metal · 10 copies · chains Q, C, R, D, S, T, F, U, A, V
- NI · Nickel (II) ion · metal · 6 copies · chains Q, R, S, T, U, V
- CA · Calcium ion · metal · 6 copies · chains Q, R, S, T, U, V
- H2S · Hydrosulfuric acid · ion · 6 copies · chains Q, R, S, T, U, V
- CO3 · Carbonate ion · ion · chains F
- GOL · Glycerol · additive · 10 copies · chains Q, A, C, B, D, R, S, T, F, E, U, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.81 | 0.82 | 118 | GOL |
| 2 | 1125 | 0.80 | 0.81 | 75 | MG |
| 3 | 1150 | 0.80 | 0.81 | 87 | MG |
| 4 | 1112 | 0.79 | 0.81 | 76 | MG |
| 5 | 1057 | 0.78 | 0.80 | 82 | MG |
Interfaces
22 interfaces between chains.
- E–U · 3603 Ų buried · 58 hydrogen bonds · protein-protein
- F–V · 3592 Ų buried · 56 hydrogen bonds · protein-protein
- B–R · 3590 Ų buried · 56 hydrogen bonds · protein-protein
- A–Q · 3585 Ų buried · 55 hydrogen bonds · protein-protein
- C–S · 3580 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, oxidation).
Compared structures
- 4UEQ · Structure of the V74C large subunit mutant of D. fructosovorans NiFe- hydrogenase · 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 4UEQ · PDBe 4UEQ · UniProt E1K248 · UniProt E1K247
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.