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Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)
Analyse Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NI4
- Type
- protein
- Length
- 1,823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukotriene a-4 hydrolase
- EC
- 3.3.2.6
- UniProt
- P09960
- Ligands
- DJ3, ZN
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leukotriene a-4 hydrolase (EC 3.3.2.6) | protein | 607 | 44% helix, 23% strand | P09960 |
| B, C | Leukotriene a-4 hydrolase (EC 3.3.2.6) | protein | 608 | 44% helix, 22% strand | P09960 |
Ligands and binding sites
- DJ3 · 5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- IMD · Imidazole · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.86 | 0.87 | 97 | ZN, IMD, DJ3 |
| 2 | 1020 | 0.86 | 0.86 | 88 | ZN, DJ3 |
| 3 | 1062 | 0.85 | 0.86 | 104 | ZN, IMD, DJ3 |
| 4 | 916 | 0.76 | 0.79 | 108 | empty |
| 5 | 714 | 0.72 | 0.78 | 52 | empty |
Interfaces
3 interfaces between chains.
- B–C · 572 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 404 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NI4 · Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II) · 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 P09960
- Elsewhere: RCSB PDB 5NI4 · PDBe 5NI4 · UniProt P09960
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