Research workbench
Crystal structure of masl in complex with a novel covalent inhibitor, collimonin C
Analyse Crystal structure of masl in complex with a novel covalent inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EI4
- Type
- protein
- Length
- 1,562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA C-acyltransferase
- EC
- 2.3.1.16
- UniProt
- A0A5C7BKK5
- Ligands
- J3U
- Pockets
- 15 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA C-acyltransferase (EC 2.3.1.16) | protein | 392 | 39% helix, 23% strand | A0A5C7BKK5 |
| B | Acetyl-CoA C-acyltransferase (EC 2.3.1.16) | protein | 389 | 39% helix, 23% strand | A0A5C7BKK5 |
| C | Acetyl-CoA C-acyltransferase (EC 2.3.1.16) | protein | 391 | 39% helix, 23% strand | A0A5C7BKK5 |
| D | Acetyl-CoA C-acyltransferase (EC 2.3.1.16) | protein | 390 | 39% helix, 23% strand | A0A5C7BKK5 |
Ligands and binding sites
- J3U · (6S,7R,9E)-6,7-bis(oxidanyl)hexadeca-9,15-dien-11,13-diynoic acid · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.60 | 0.83 | 35 | J3U |
| 2 | 129 | 0.59 | 0.84 | 27 | J3U |
| 3 | 154 | 0.59 | 0.83 | 35 | J3U |
| 4 | 164 | 0.59 | 0.82 | 34 | J3U |
| 5 | 106 | 0.42 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2620 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 2582 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 804 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 800 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7EI4 · Crystal structure of MasL in complex with a novel covalent inhibitor, collimonin C · 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 A0A5C7BKK5
- Elsewhere: RCSB PDB 7EI4 · PDBe 7EI4 · UniProt A0A5C7BKK5
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