Research workbench
Crystal structure of [nife] hydrogenase maturation protein hypb from thermococcus kodakarensis KOD1
Analyse Crystal structure of [nife] hydrogenase maturation protein hypb from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VX3
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPase involved in chromosome partitioning, PARA/MIND family, mrp homolog
- UniProt
- Q5JIH4
- Ligands
- ADP
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATPase involved in chromosome partitioning, PARA/MIND family, mrp homolog | protein | 235 | 39% helix, 24% strand | Q5JIH4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.88 | 0.90 | 113 | ADP, EDO |
| 2 | 59 | 0.39 | 0.80 | 9 | empty |
| 3 | 71 | 0.36 | 0.76 | 13 | empty |
| 4 | 57 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VX3 · Crystal structure of [NiFe] hydrogenase maturation protein HypB 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 Q5JIH4
- Elsewhere: RCSB PDB 3VX3 · PDBe 3VX3 · UniProt Q5JIH4
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