SMTL ID : 3rde.5 (4 other biounits)

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: T.26, D.29, H.393 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.29, A:H.393, H2O.8 K.8: 3 residues within 4Å: Chain D: L.192, I.195, V.209 No protein-ligand interaction detected (PLIP)

4 x FE2: FE (II) ION(Non-covalent)

FE2.2: 5 residues within 4Å: Chain A: H.271, H.276, H.451, H.455, I.573 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.271, A:H.276, A:H.451, A:H.455, H2O.1 FE2.4: 5 residues within 4Å: Chain B: H.271, H.276, H.451, H.455, I.573 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.271, B:H.276, B:H.451, B:H.455, H2O.16 FE2.6: 5 residues within 4Å: Chain C: H.271, H.276, H.451, H.455, I.573 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.271, C:H.276, C:H.451, C:H.455, H2O.30 FE2.9: 5 residues within 4Å: Chain D: H.271, H.276, H.451, H.455, I.573 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.271, D:H.276, D:H.451, D:H.455, H2O.38

4 x OYP: 3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid(Non-covalent)

OYP.3: 20 residues within 4Å: Chain A: F.85, L.89, E.267, H.271, L.272, H.276, I.310, R.313, A.314, G.317, L.318, I.324, V.328, Q.458, Q.500, I.503, T.504, Q.506, L.507, I.573 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.85, A:L.89, A:L.272, A:L.318, A:L.318, A:L.318, A:L.318, A:I.324, A:V.328, A:Q.500, A:I.503, A:T.504, A:L.507, A:L.507 Hydrogen bonds: A:Q.506 OYP.5: 20 residues within 4Å: Chain B: F.85, L.89, F.263, E.267, H.271, L.272, H.276, I.310, R.313, A.314, G.317, L.318, I.324, V.328, V.329, Q.500, I.503, Q.506, L.507, I.573 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.263, B:L.272, B:R.313, B:L.318, B:L.318, B:L.318, B:I.324, B:V.328, B:V.329, B:I.503, B:L.507 Hydrogen bonds: B:Q.506 OYP.7: 21 residues within 4Å: Chain C: F.85, L.89, F.263, E.267, H.271, L.272, H.276, I.310, R.313, A.314, G.317, L.318, I.324, V.328, V.329, Q.458, Q.500, I.503, Q.506, L.507, I.573 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.85, C:L.89, C:F.263, C:L.272, C:R.313, C:L.318, C:L.318, C:I.324, C:V.328, C:V.329, C:I.503, C:L.507 Hydrogen bonds: C:Q.506 OYP.10: 19 residues within 4Å: Chain D: L.89, F.263, E.267, H.271, L.272, H.276, I.310, R.313, A.314, G.317, L.318, I.324, V.328, V.329, Q.458, Q.500, I.503, L.507, I.573 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.263, D:L.272, D:R.313, D:L.318, D:L.318, D:I.324, D:V.328, D:V.329, D:I.503, D:L.507, D:L.507

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Crystal structure of 12-lipoxygenase catalytic-domain-inhibitor complex identifies a substrate-binding channel for catalysis. Structure (2012)

Release Date

2012-04-18

Peptides

Arachidonate 12-lipoxygenase, 12S-type: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Arachidonate 12-lipoxygenase, 12S-type

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