MolNFT v1 · #161497 · protein
Petase from ideonella sakaiensis without ligand
6QGC · POLY(ETHYLENE terephthalate) hydrolase: “Petase from ideonella sakaiensis without ligand”. X-ray diffraction, 2 ligands (CL, SO4), 2 pockets (best druggability 0.51). MolNFT v1 #161497 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QGC
- Type
- protein
- Length
- 1,046 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ETHYLENE terephthalate) hydrolase
- EC
- 3.1.1.101
- UniProt
- A0A0K8P6T7
- Ligands
- CL, SO4
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ETHYLENE terephthalate) hydrolase (EC 3.1.1.101) | protein | 262 | 29% helix, 22% strand | A0A0K8P6T7 |
| B, D | POLY(ETHYLENE terephthalate) hydrolase (EC 3.1.1.101) | protein | 261 | 31% helix, 22% strand | A0A0K8P6T7 |
| C | POLY(ETHYLENE terephthalate) hydrolase (EC 3.1.1.101) | protein | 262 | 30% helix, 23% strand | A0A0K8P6T7 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.51 | 0.78 | 26 | CL |
| 2 | 97 | 0.34 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 498 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6QGC · PETase from Ideonella sakaiensis without ligand · 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 A0A0K8P6T7
- Elsewhere: RCSB PDB 6QGC · PDBe 6QGC · UniProt A0A0K8P6T7
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