Research workbench
High-resolution structure of a ni-a ni-sox mixture of the D. fructosovorans nife-hydrogenase L122A mutant
Analyse High-resolution structure of a ni-a ni-sox mixture of the D. fructosovorans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UQL
- Type
- protein
- Length
- 1,614 residues
- Chains
- 4
- 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, GLY, F3S, FCO, SOT, NI, MG, H2S, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 262 | 37% helix, 16% strand | E1K248 |
| B | Hydrogenase (nife) small subunit hyda (EC 1.12.2.1) | protein | 263 | 37% helix, 17% strand | E1K248 |
| Q | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 544 | 49% helix, 16% strand | E1K247 |
| R | Nickel-dependent hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 49% helix, 15% strand | E1K247 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, Q, B, R
- GLY · Glycine · ligand · 3 copies · chains B, A, Q, R
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, Q, B, R
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains Q, R
- SOT · morpholine-4-sulfonic acid · ligand · chains B
- NI · Nickel (II) ion · metal · 2 copies · chains Q, R
- MG · Magnesium ion · metal · 2 copies · chains Q, R
- H2S · Hydrosulfuric acid · ion · chains B, R
- CL · Chloride ion · ion · chains Q
- GOL · Glycerol · additive · 11 copies · chains A, Q, B, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.84 | 0.97 | 63 | GLY |
| 2 | 163 | 0.81 | 0.96 | 42 | GLY |
| 3 | 974 | 0.76 | 0.79 | 76 | empty |
| 4 | 50 | 0.59 | 0.92 | 20 | empty |
| 5 | 52 | 0.58 | 0.91 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–Q · 3560 Ų buried · 58 hydrogen bonds · protein-protein
- B–R · 3533 Ų buried · 58 hydrogen bonds · protein-protein
- Q–R · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide, 1 covalent (oxidation, disulfide, covalent ligand).
Compared structures
- 4UQL · High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans… · the same entry in another collection · chain Q against Q, 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 4UQL · PDBe 4UQL · UniProt E1K248 · UniProt E1K247
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