Research workbench
Crystal structure of ideonella sakaiensis mhetase
Analyse Crystal structure of ideonella sakaiensis mhetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QG9
- Type
- protein
- Length
- 5,588 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MONO(2-hydroxyethyl) terephthalate hydrolase
- EC
- 3.1.1.102
- UniProt
- A0A0K8P8E7
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, I | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 559 | 33% helix, 19% strand | A0A0K8P8E7 |
| E | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 560 | 33% helix, 19% strand | A0A0K8P8E7 |
| G | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 562 | 34% helix, 19% strand | A0A0K8P8E7 |
| H | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 557 | 34% helix, 19% strand | A0A0K8P8E7 |
| J | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 555 | 33% helix, 19% strand | A0A0K8P8E7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 11 copies · chains A, F, B, C, D, E, G, H, I
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- ACT · Acetate ion · additive · 2 copies · chains D, F
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.85 | 0.86 | 106 | empty |
| 2 | 1000 | 0.84 | 0.86 | 106 | empty |
| 3 | 811 | 0.80 | 0.83 | 98 | empty |
| 4 | 579 | 0.80 | 0.86 | 61 | empty |
| 5 | 1141 | 0.78 | 0.80 | 117 | empty |
Interfaces
16 interfaces between chains.
- C–F · 904 Ų buried · 14 hydrogen bonds · protein-protein
- H–J · 816 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 814 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 793 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 786 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide (disulfide).
Compared structures
- 6QG9 · Crystal structure of Ideonella sakaiensis MHETase · 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 A0A0K8P8E7
- Elsewhere: RCSB PDB 6QG9 · PDBe 6QG9 · UniProt A0A0K8P8E7
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