Research workbench
Staphylopine dehydrogenase in complex with histidine tag and citrate
Analyse Staphylopine dehydrogenase in complex with histidine tag and citrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GMZ
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylopine dehydrogenase; Ala-his-his-ala
- UniProt
- A0A1Q4GXD5
- Ligands
- NH4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylopine dehydrogenase | protein | 428 | 47% helix, 16% strand | A0A1Q4GXD5 |
| B | Ala-his-his-ala | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · chains A, B
- CIT · Citric acid · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.81 | 0.94 | 26 | PG4 |
| 2 | 1051 | 0.79 | 0.81 | 96 | NH4, CIT |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 6GMZ · Staphylopine dehydrogenase in complex with Histidine tag and citrate · 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 A0A1Q4GXD5
- Elsewhere: RCSB PDB 6GMZ · PDBe 6GMZ · UniProt A0A1Q4GXD5
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