Research workbench
High-resolution structure of anaerobically purified dm. baculatum [nifese]-hydrogenase after crystallization under air
Analyse High-resolution structure of anaerobically purified dm. baculatum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KL8
- Type
- protein
- Length
- 1,536 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic [nifese] hydrogenase small subunit; Nickel-dependent hydrogenase large subunit
- EC
- 1.12.99.6
- UniProt
- P13063, C7LN88
- Ligands
- SF4, FCO, CA, NI, H2S, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S, T | Periplasmic [nifese] hydrogenase small subunit (EC 1.12.99.6) | protein | 279 | 38% helix, 19% strand | P13063 |
| L, M | Nickel-dependent hydrogenase large subunit (EC 1.12.99.6) | protein | 489 | 44% helix, 19% strand | C7LN88 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains S, L, T, M
- FCO · Carbonmonoxide-(dicyano) iron · ligand · 2 copies · chains L, M
- CA · Calcium ion · metal · 8 copies · chains S, L, T, M
- NI · Nickel (II) ion · metal · 2 copies · chains L, M
- H2S · Hydrosulfuric acid · ion · 2 copies · chains L, M
- CL · Chloride ion · ion · chains S
- GOL · Glycerol · additive · 4 copies · chains S, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.77 | 0.81 | 78 | CL, GOL, CA |
| 2 | 77 | 0.75 | 0.97 | 39 | empty |
| 3 | 54 | 0.72 | 0.98 | 26 | empty |
| 4 | 229 | 0.65 | 0.83 | 30 | empty |
| 5 | 159 | 0.53 | 0.79 | 22 | empty |
Interfaces
4 interfaces between chains.
- T–M · 3405 Ų buried · 63 hydrogen bonds · protein-protein
- S–L · 3366 Ų buried · 58 hydrogen bonds · protein-protein
- L–M · 268 Ų buried · 0 hydrogen bonds · protein-protein
- S–M · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4KL8 · High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase… · the same entry in another collection · chain S against S, TM-score 1.00
- P13063 · AlphaFold monomer V2.0 prediction for periplasmic [nifese] hydrogenase small subunit… · a predicted model of the same protein · chain S 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 P13063
- Every structure of UniProt C7LN88
- Elsewhere: RCSB PDB 4KL8 · PDBe 4KL8 · UniProt P13063 · UniProt C7LN88
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