MolNFT v1 · #12716 · protein
Crystal structure of mycolic acid cyclopropane synthase CMAA1 complexed with sah and ctab
1KPG · Cyclopropane-fatty-acyl-phospholipid synthase 1: “Crystal structure of mycolic acid cyclopropane synthase CMAA1 complexed with sah and ctab”. X-ray diffraction, 3 ligands (SAH, 16A, CO3), 11 pockets (best druggability 0.86). MolNFT…
- PDB
- 1KPG
- Type
- protein
- Length
- 1,137 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, 16A, CO3
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclopropane-fatty-acyl-phospholipid synthase 1 (EC 2.1.1.79) | protein | 285 | 47% helix, 16% strand | Q11195 |
| B | Cyclopropane-fatty-acyl-phospholipid synthase 1 (EC 2.1.1.79) | protein | 284 | 49% helix, 17% strand | Q11195 |
| D | Cyclopropane-fatty-acyl-phospholipid synthase 1 (EC 2.1.1.79) | protein | 283 | 49% helix, 16% strand | Q11195 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- 16A · Cetyl-trimethyl-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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.86 | 0.93 | 64 | CO3, SAH, 16A |
| 2 | 378 | 0.86 | 0.94 | 58 | CO3, SAH, 16A |
| 3 | 1060 | 0.81 | 0.83 | 100 | empty |
| 4 | 166 | 0.81 | 0.97 | 35 | SAH |
| 5 | 163 | 0.80 | 0.96 | 33 | SAH |
Interfaces
6 interfaces between chains.
- A–C · 684 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 352 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 199 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1KPG · Crystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and CTAB · 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 1KPG · PDBe 1KPG · UniProt Q11195
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