Research workbench
Crystal structure of AG85C bound to cyclophostin 8BETA inhibitor
Analyse Crystal structure of AG85C bound to cyclophostin 8BETA inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCJ
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C
- EC
- 2.3.1.122, 2.3.1.20
- UniProt
- P9WQN9
- Ligands
- 9SW
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C (EC 2.3.1.122, 2.3.1.20) | protein | 275 | 39% helix, 16% strand | P9WQN9 |
| B | Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C (EC 2.3.1.122, 2.3.1.20) | protein | 277 | 39% helix, 17% strand | P9WQN9 |
Ligands and binding sites
- 9SW · methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.78 | 0.82 | 66 | 9SW |
| 2 | 99 | 0.35 | 0.74 | 21 | empty |
| 3 | 55 | 0.35 | 0.78 | 13 | empty |
| 4 | 51 | 0.33 | 0.78 | 11 | empty |
| 5 | 60 | 0.26 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 912 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5OCJ · Crystal structure of Ag85C bound to cyclophostin 8beta inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P9WQN9 · AlphaFold monomer V2.0 prediction for diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE… · a predicted model of the same protein · chain B 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 P9WQN9
- Elsewhere: RCSB PDB 5OCJ · PDBe 5OCJ · UniProt P9WQN9
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