Research workbench
Hydrolase stna mutant - S185A
Analyse Hydrolase stna mutant - S185A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDP
- Type
- protein
- Length
- 2,210 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase
- UniProt
- L7PIJ2
- Ligands
- STM
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C, E, G | Hydrolase | protein | 316 | 35% helix, 21% strand | L7PIJ2 |
| F | Hydrolase | protein | 314 | 35% helix, 19% strand | L7PIJ2 |
Ligands and binding sites
- STM · methyl 5-amino-6-(7-amino-6-methoxy-5,8-dioxo-5,8-dihydroquinolin-2-yl)-4-(2-hydroxy-3-methoxyphenyl)-3-methylpyridine-2-carboxylate · ligand · 7 copies · chains D, A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.75 | 0.88 | 45 | empty |
| 2 | 287 | 0.72 | 0.86 | 50 | empty |
| 3 | 969 | 0.70 | 0.75 | 67 | empty |
| 4 | 272 | 0.69 | 0.84 | 32 | STM |
| 5 | 254 | 0.68 | 0.84 | 32 | STM |
Interfaces
8 interfaces between chains.
- A–B · 657 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 641 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 531 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 530 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 268 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5HDP · Hydrolase StnA mutant - S185A · the same entry in another collection · chain D against D, 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 L7PIJ2
- Elsewhere: RCSB PDB 5HDP · PDBe 5HDP · UniProt L7PIJ2
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