Research workbench
Crystal structure of a methylesterase protein MES16 from arabidopsis
Analyse Crystal structure of a methylesterase protein MES16 from arabidopsis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HK8
- Type
- protein
- Length
- 1,416 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable pheophorbidase
- EC
- 3.1.1.82
- UniProt
- O23512
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Probable pheophorbidase (EC 3.1.1.82) | protein | 236 | 38% helix, 18% strand | O23512 |
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.80 | 0.81 | 83 | empty |
| 2 | 1126 | 0.76 | 0.78 | 107 | empty |
| 3 | 195 | 0.49 | 0.75 | 26 | empty |
| 4 | 170 | 0.48 | 0.77 | 24 | empty |
| 5 | 169 | 0.47 | 0.76 | 24 | empty |
Interfaces
10 interfaces between chains.
- E–F · 994 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 987 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 394 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HK8 · Crystal structure of a methylesterase protein MES16 from Arabidopsis · the same entry in another collection · chain C against C, TM-score 1.00
- O23512 · AlphaFold monomer V2.0 prediction for probable pheophorbidase (O23512) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O23512
- Elsewhere: RCSB PDB 5HK8 · PDBe 5HK8 · UniProt O23512
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