MolNFT v1 · #128156 · protein
Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)
5NI4 · Leukotriene a-4 hydrolase: “Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)”. X-ray diffraction, 2 ligands (DJ3, ZN), 16 pockets (best druggability 0.86). MolNFT v1 #128156 on GenesisL1: 3D…
- 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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