MolNFT v1 · #161496 · protein
Crystal structure of ideonella sakaiensis mhetase bound to benzoic acid
6QGB · MONO(2-hydroxyethyl) terephthalate hydrolase: “Crystal structure of ideonella sakaiensis mhetase bound to benzoic acid”. X-ray diffraction, 4 ligands (BEZ, CA, SO4), 16 pockets (best druggability 0.83). MolNFT v1 #161496 on…
- PDB
- 6QGB
- Type
- protein
- Length
- 3,345 residues
- Chains
- 6
- 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
- BEZ, CA, SO4, CL
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 557 | 34% helix, 19% strand | A0A0K8P8E7 |
| B | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 559 | 34% helix, 18% strand | A0A0K8P8E7 |
| C | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 558 | 33% helix, 18% strand | A0A0K8P8E7 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 10 copies · chains A, D, B, E, C, F
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.83 | 0.84 | 101 | empty |
| 2 | 1199 | 0.83 | 0.84 | 116 | SO4 |
| 3 | 793 | 0.82 | 0.85 | 90 | SO4 |
| 4 | 852 | 0.81 | 0.84 | 94 | SO4 |
| 5 | 55 | 0.64 | 0.93 | 22 | BEZ |
Interfaces
4 interfaces between chains.
- A–D · 784 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 759 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 723 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 702 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 6QGB · Crystal structure of Ideonella sakaiensis MHETase bound to benzoic acid · 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 6QGB · PDBe 6QGB · UniProt A0A0K8P8E7
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