Research workbench
Crystal structure of [nife] hydrogenase maturation protein, hypd from thermococcus kodakaraensis
Analyse Crystal structure of [nife] hydrogenase maturation protein, hypd from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z1D
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase EXPRESSION/FORMATION protein hypd
- UniProt
- Q5JII1
- Ligands
- SF4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrogenase EXPRESSION/FORMATION protein hypd | protein | 366 | 45% helix, 19% strand | Q5JII1 |
| B | Hydrogenase EXPRESSION/FORMATION protein hypd | protein | 368 | 45% helix, 18% strand | Q5JII1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.76 | 0.78 | 62 | empty |
| 2 | 137 | 0.50 | 0.79 | 23 | empty |
| 3 | 118 | 0.48 | 0.79 | 21 | empty |
| 4 | 56 | 0.31 | 0.76 | 16 | empty |
| 5 | 56 | 0.25 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 262 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 2Z1D · Crystal structure of [NiFe] hydrogenase maturation protein, HypD from Thermococcus… · 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 Q5JII1
- Elsewhere: RCSB PDB 2Z1D · PDBe 2Z1D · UniProt Q5JII1
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