MolNFT v1 · #12717 · protein
Crystal structure of mycolic acid cyclopropane synthase CMAA1 complexed with sah and dddmab
1KPH · Cyclopropane-fatty-acyl-phospholipid synthase 1: “Crystal structure of mycolic acid cyclopropane synthase CMAA1 complexed with sah and dddmab”. X-ray diffraction, 3 ligands (SAH, 10A, CO3), 11 pockets (best druggability 0.84).…
- PDB
- 1KPH
- Type
- protein
- Length
- 1,138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclopropane-fatty-acyl-phospholipid synthase 1
- EC
- 2.1.1.79
- UniProt
- Q11195
- Ligands
- SAH, 10A, CO3
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclopropane-fatty-acyl-phospholipid synthase 1 (EC 2.1.1.79) | protein | 283 | 51% helix, 16% strand | Q11195 |
| B, C, D | Cyclopropane-fatty-acyl-phospholipid synthase 1 (EC 2.1.1.79) | protein | 285 | 49% helix, 16% strand | Q11195 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- 10A · Didecyl-dimethyl-ammonium · ligand · 4 copies · chains A, B, C, D
- CO3 · Carbonate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.84 | 0.91 | 68 | CO3, SAH, 10A |
| 2 | 442 | 0.84 | 0.91 | 63 | CO3, SAH, 10A |
| 3 | 445 | 0.84 | 0.91 | 66 | CO3, SAH, 10A |
| 4 | 443 | 0.81 | 0.89 | 48 | empty |
| 5 | 159 | 0.79 | 0.95 | 36 | SAH |
Interfaces
3 interfaces between chains.
- A–D · 651 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 429 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 184 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1KPH · Crystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and… · 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 Q11195
- Elsewhere: RCSB PDB 1KPH · PDBe 1KPH · UniProt Q11195
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