MolNFT v1 · #58315 · protein
Crystal structure of puromycin hydrolase S511A mutant complexed with pgg
3AZQ · Aminopeptidase: “Crystal structure of puromycin hydrolase S511A mutant complexed with pgg”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.83). MolNFT v1 #58315 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3AZQ
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase; Tripeptide pgg
- UniProt
- Q2HXD9
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminopeptidase | protein | 661 | 16% helix, 33% strand | Q2HXD9 |
| C, D | Tripeptide pgg | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.83 | 0.86 | 97 | empty |
| 2 | 719 | 0.82 | 0.86 | 87 | SO4 |
| 3 | 1126 | 0.80 | 0.81 | 66 | empty |
| 4 | 502 | 0.72 | 0.82 | 81 | empty |
| 5 | 473 | 0.68 | 0.79 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 665 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 150 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3AZQ · Crystal structure of puromycin hydrolase S511A mutant complexed with PGG · 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 Q2HXD9
- Elsewhere: RCSB PDB 3AZQ · PDBe 3AZQ · UniProt Q2HXD9
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