Research workbench
Crystal structure of AP4A hydrolase (AQ_158) from aquifex aeolicus VF5
Analyse Crystal structure of AP4A hydrolase (AQ_158) from aquifex aeolicus VF5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7U
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AP4A hydrolase
- UniProt
- O66548
- Ligands
- CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AP4A hydrolase | protein | 133 | 28% helix, 49% strand | O66548 |
| C, D | AP4A hydrolase | protein | 134 | 28% helix, 47% strand | O66548 |
Ligands and binding sites
- CL · Chloride ion · ion · 11 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, D, C
- PGE · Triethylene glycol · additive · 2 copies · chains D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, D
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.82 | 0.83 | 100 | CL, EDO, PEG |
| 2 | 80 | 0.64 | 0.91 | 16 | empty |
| 3 | 177 | 0.45 | 0.75 | 25 | CL, PEG, PGE |
| 4 | 161 | 0.45 | 0.75 | 24 | CL |
| 5 | 162 | 0.43 | 0.74 | 24 | EDO |
Interfaces
5 interfaces between chains.
- B–C · 875 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 547 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 472 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3I7U · Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5 · 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 O66548
- Elsewhere: RCSB PDB 3I7U · PDBe 3I7U · UniProt O66548
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