Research workbench
Crystal structure of a had-superfamily hydrolase, subfamily ia, variant 1 (GSU2069) from geobacter sulfurreducens pca at 2.15 a resolution
Analyse Crystal structure of a had-superfamily hydrolase, subfamily ia, variant 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RN3
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Had superfamily hydrolase
- UniProt
- Q74BH2
- Ligands
- MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Had superfamily hydrolase | protein | 210 | 46% helix, 15% strand | Q74BH2 |
| B | Had superfamily hydrolase | protein | 193 | 45% helix, 16% strand | Q74BH2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.66 | 0.78 | 45 | MG |
| 2 | 623 | 0.64 | 0.74 | 45 | empty |
| 3 | 64 | 0.39 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 4RN3 · Crystal structure of a HAD-superfamily hydrolase, subfamily IA, variant 1 (GSU2069) from… · 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 Q74BH2
- Elsewhere: RCSB PDB 4RN3 · PDBe 4RN3 · UniProt Q74BH2
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