Research workbench
Structure of a double methionine mutant of ni-fe hydrogenase
Analyse Structure of a double methionine mutant of ni-fe hydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CUR
- Type
- protein
- Length
- 2,419 residues
- Chains
- 6
- 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
- P18187, P18188
- Ligands
- SF4, F3S, FCO, NI, MG, PER
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 262 | 37% helix, 17% strand | P18187 |
| H, I, J | Periplasmic [nife] hydrogenase large subunit (EC 1.12.2.1) | protein | 545 | 48% helix, 16% strand | P18188 |
| C | Periplasmic [nife] hydrogenase small subunit (EC 1.12.2.1) | protein | 260 | 37% helix, 17% strand | P18187 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, H, B, I, C, J
- F3S · FE3-S4 cluster · ligand · 3 copies · chains A, H, B, I, C, J
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 3 copies · chains H, I, J
- NI · Nickel (II) ion · metal · 3 copies · chains H, I, J
- MG · Magnesium ion · metal · 3 copies · chains H, I, J
- PER · Peroxide ion · ion · 3 copies · chains H, I, J
- GOL · Glycerol · additive · 7 copies · chains H, A, C, B, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.80 | 0.82 | 73 | empty |
| 2 | 791 | 0.77 | 0.81 | 98 | empty |
| 3 | 82 | 0.76 | 0.97 | 28 | empty |
| 4 | 91 | 0.76 | 0.96 | 32 | empty |
| 5 | 88 | 0.75 | 0.96 | 35 | empty |
Interfaces
8 interfaces between chains.
- B–I · 3594 Ų buried · 55 hydrogen bonds · protein-protein
- A–H · 3583 Ų buried · 58 hydrogen bonds · protein-protein
- C–J · 3564 Ų buried · 56 hydrogen bonds · protein-protein
- I–C · 526 Ų buried · 8 hydrogen bonds · protein-protein
- H–C · 468 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3CUR · Structure of a double methionine mutant of NI-FE hydrogenase · the same entry in another collection · chain J against J, TM-score 1.00
- P18188 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase large subunit… · a predicted model of the same protein · chain H against A, TM-score 1.00
- P18187 · AlphaFold monomer V2.0 prediction for periplasmic [nife] hydrogenase small subunit… · a predicted model of the same protein · chain C 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 P18187
- Every structure of UniProt P18188
- Elsewhere: RCSB PDB 3CUR · PDBe 3CUR · UniProt P18187 · UniProt P18188
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