Research workbench
Crystal structure of LTC4S in complex with AZ13690257
Analyse Crystal structure of LTC4S in complex with AZ13690257 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R7D
- Type
- protein
- Length
- 1,790 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukotriene C4 synthase
- EC
- 4.4.1.20
- UniProt
- Q16873
- Ligands
- PLM, JUQ, NI
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, J | Leukotriene C4 synthase (EC 4.4.1.20) | protein | 149 | 85% helix, 0% strand | Q16873 |
| C, I, L | Leukotriene C4 synthase (EC 4.4.1.20) | protein | 148 | 84% helix, 0% strand | Q16873 |
| D, F, K | Leukotriene C4 synthase (EC 4.4.1.20) | protein | 150 | 85% helix, 0% strand | Q16873 |
| H | Leukotriene C4 synthase (EC 4.4.1.20) | protein | 151 | 83% helix, 0% strand | Q16873 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 43 copies · chains A, C, B, E, D, F, G, H, I, J, L, K
- JUQ · (1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl) amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid · ligand · 12 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- NI · Nickel (II) ion · metal · 8 copies · chains A, B, C, F, D, E, G, H, I, J, K, L
- LMT · Dodecyl-beta-D-maltoside · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.85 | 0.87 | 59 | PLM |
| 2 | 882 | 0.85 | 0.86 | 58 | PLM |
| 3 | 876 | 0.85 | 0.86 | 59 | PLM |
| 4 | 870 | 0.85 | 0.86 | 57 | PLM |
| 5 | 246 | 0.74 | 0.88 | 33 | empty |
Interfaces
19 interfaces between chains.
- D–E · 1155 Ų buried · 8 hydrogen bonds · protein-protein
- G–I · 1154 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 1152 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1150 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6R7D · Crystal structure of LTC4S in complex with AZ13690257 · the same entry in another collection · chain L against L, 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 Q16873
- Elsewhere: RCSB PDB 6R7D · PDBe 6R7D · UniProt Q16873
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