MolNFT v1 · #161495 · protein
Crystal structure of ideonella sakaiensis mhetase bound to the non- hydrolyzable ligand mheta
6QGA · MONO(2-hydroxyethyl) terephthalate hydrolase: “Crystal structure of ideonella sakaiensis mhetase bound to the non- hydrolyzable ligand mheta”. X-ray diffraction, 4 ligands (J1K, CA, SO4), 11 pockets (best druggability 0.84). MolNFT…
- PDB
- 6QGA
- Type
- protein
- Length
- 3,349 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
- J1K, CA, SO4, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 558 | 33% helix, 19% strand | A0A0K8P8E7 |
| B, E | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 558 | 33% helix, 18% strand | A0A0K8P8E7 |
| C | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 557 | 33% helix, 19% strand | A0A0K8P8E7 |
| D, F | MONO(2-hydroxyethyl) terephthalate hydrolase (EC 3.1.1.102) | protein | 559 | 33% helix, 18% strand | A0A0K8P8E7 |
Ligands and binding sites
- J1K · 4-(2-hydroxyethylcarbamoyl)benzoic acid · ligand · 10 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, F, B, C, E
- CL · Chloride ion · ion · 4 copies · chains B, C, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.84 | 0.86 | 96 | SO4, MPD, J1K |
| 2 | 1009 | 0.84 | 0.85 | 109 | SO4, J1K |
| 3 | 883 | 0.83 | 0.85 | 96 | SO4, J1K |
| 4 | 780 | 0.81 | 0.85 | 92 | SO4 |
| 5 | 57 | 0.64 | 0.93 | 22 | J1K |
Interfaces
4 interfaces between chains.
- A–D · 803 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 773 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 680 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 679 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 6QGA · Crystal structure of Ideonella sakaiensis MHETase bound to the non-hydrolyzable 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 A0A0K8P8E7
- Elsewhere: RCSB PDB 6QGA · PDBe 6QGA · UniProt A0A0K8P8E7
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