SMTL ID : 5ni4.1

Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.302, H.306, E.325, T.328, Y.390 Ligands: DJ3.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.302, A:H.306, A:E.325, A:E.325, H2O.1 ZN.6: 6 residues within 4Å: Chain B: H.302, H.306, E.325, T.328, Y.390 Ligands: DJ3.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.302, B:H.306, B:E.325, B:E.325, H2O.27 ZN.11: 6 residues within 4Å: Chain C: H.302, H.306, E.325, T.328, Y.390 Ligands: DJ3.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.302, C:H.306, C:E.325, C:E.325, H2O.54

7 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 8 residues within 4Å: Chain A: G.351, G.354, E.355, N.358, E.508, A.511, Q.512, Q.515 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.355, A:E.355, A:E.508 Water bridges: A:G.354 IMD.3: 10 residues within 4Å: Chain A: G.255, G.256, P.257, V.259, W.308, L.312, V.418, E.419, S.422, Y.423 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.255, A:W.308, A:S.422 Water bridges: A:E.419 IMD.4: 2 residues within 4Å: Chain A: D.429, D.433 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.433 IMD.7: 8 residues within 4Å: Chain B: G.351, G.354, E.355, N.358, E.508, A.511, Q.512, Q.515 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.358, B:E.508 Water bridges: B:G.354, B:N.358, B:A.511 IMD.8: 3 residues within 4Å: Chain B: E.9, D.429, D.433 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.433 IMD.9: 10 residues within 4Å: Chain B: G.255, G.256, P.257, V.259, W.308, L.312, V.418, E.419, S.422, Y.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.255, B:S.422 IMD.12: 9 residues within 4Å: Chain C: G.351, G.354, E.355, N.358, E.508, A.511, Q.512, Q.515, R.544 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.355, C:E.355, C:E.508 Water bridges: C:G.354, C:R.544

3 x DJ3: 5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid(Non-covalent)

DJ3.5: 27 residues within 4Å: Chain A: Q.141, Q.143, A.144, Y.274, G.275, G.276, M.277, H.302, E.303, H.306, W.318, D.319, F.321, W.322, E.325, L.372, V.374, L.376, P.381, D.382, A.384, Y.385, P.389, Y.390, R.570, K.572 Ligands: ZN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.143, A:Y.274, A:F.321, A:F.321, A:F.321, A:V.374, A:Y.385, A:Y.385, A:P.389 Hydrogen bonds: A:G.275, A:Y.390 Water bridges: A:K.572 Salt bridges: A:R.570, A:K.572 DJ3.10: 27 residues within 4Å: Chain B: Q.141, Q.143, A.144, Y.274, G.275, G.276, M.277, H.302, E.303, H.306, W.318, D.319, F.321, W.322, E.325, L.372, V.374, L.376, P.381, D.382, A.384, Y.385, P.389, Y.390, R.570, K.572 Ligands: ZN.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Q.143, B:A.144, B:Y.274, B:F.321, B:F.321, B:F.321, B:V.374, B:P.381, B:Y.385, B:Y.385 Hydrogen bonds: B:G.275, B:Y.390 Salt bridges: B:R.570, B:K.572 DJ3.13: 24 residues within 4Å: Chain C: Q.141, Q.143, A.144, Y.274, G.275, G.276, M.277, H.302, E.303, H.306, W.318, F.321, E.325, V.374, L.376, P.381, D.382, A.384, Y.385, P.389, Y.390, R.570, K.572 Ligands: ZN.11 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Q.143, C:A.144, C:Y.274, C:F.321, C:F.321, C:F.321, C:V.374, C:P.381, C:Y.385, C:Y.385, C:P.389 Hydrogen bonds: C:G.275 Water bridges: C:K.572, C:K.572 Salt bridges: C:R.570, C:K.572

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stsiapanava, A. et al., Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-23

Peptides

Leukotriene A-4 hydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Leukotriene A-4 hydrolase

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