Research workbench
Crystal structure of hydrogenase 2 maturation peptidase from thaumarchaeota archaeon SCGC_AB-539-E09
Analyse Crystal structure of hydrogenase 2 maturation peptidase from thaumarchaeota… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TTX
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrogenase 2 maturation peptidase
- UniProt
- M7TUZ8
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydrogenase 2 maturation peptidase | protein | 154 | 38% helix, 24% strand | M7TUZ8 |
| C | Hydrogenase 2 maturation peptidase | protein | 151 | 40% helix, 25% strand | M7TUZ8 |
| D | Hydrogenase 2 maturation peptidase | protein | 153 | 39% helix, 25% strand | M7TUZ8 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.53 | 0.78 | 26 | empty |
| 2 | 79 | 0.35 | 0.76 | 19 | empty |
| 3 | 61 | 0.30 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1559 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1423 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5TTX · Crystal structure of hydrogenase 2 maturation peptidase from Thaumarchaeota archaeon… · 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 M7TUZ8
- Elsewhere: RCSB PDB 5TTX · PDBe 5TTX · UniProt M7TUZ8
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