SMTL ID : 8ghd.1

The structure of h12-LOX in hexameric form bound to inhibitor ML355 and arachidonic acid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.366, A:H.371, A:H.546, A:I.669 FE2.4: 5 residues within 4Å: Chain B: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.366, B:H.371, B:H.546, B:I.669 FE2.7: 5 residues within 4Å: Chain C: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.366, C:H.371, C:H.546, C:I.669 FE2.10: 5 residues within 4Å: Chain D: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.366, D:H.371, D:H.546, D:I.669 FE2.13: 5 residues within 4Å: Chain E: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.366, E:H.371, E:H.546, E:I.669 FE2.16: 5 residues within 4Å: Chain F: H.366, H.371, H.546, N.550, I.669 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.366, F:H.371, F:H.546, F:I.669

6 x ZR5: N-(1,3-benzothiazol-2-yl)-4-{[(2-hydroxy-3-methoxyphenyl)methyl]amino}benzene-1-sulfonamide(Non-covalent)

ZR5.2: 15 residues within 4Å: Chain A: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.419, A:I.419, A:L.595, A:L.595, A:A.598, A:I.599 Hydrogen bonds: A:L.184, A:R.195, A:R.296, A:R.591 ZR5.5: 15 residues within 4Å: Chain B: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.419, B:I.419, B:L.595, B:L.595, B:A.598, B:I.599 Hydrogen bonds: B:L.184, B:R.195, B:R.296, B:R.591 ZR5.8: 15 residues within 4Å: Chain C: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.419, C:I.419, C:L.595, C:L.595, C:A.598, C:I.599 Hydrogen bonds: C:L.184, C:R.195, C:R.296, C:R.591 ZR5.11: 15 residues within 4Å: Chain D: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.12 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.419, D:I.419, D:L.595, D:L.595, D:A.598, D:I.599 Hydrogen bonds: D:L.184, D:R.195, D:R.296, D:R.591 ZR5.14: 15 residues within 4Å: Chain E: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.15 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:I.419, E:I.419, E:L.595, E:L.595, E:A.598, E:I.599 Hydrogen bonds: E:L.184, E:R.195, E:R.296, E:R.591 ZR5.17: 15 residues within 4Å: Chain F: T.183, L.184, G.187, A.188, M.191, R.195, R.296, I.419, K.422, R.591, L.595, A.598, I.599, H.602 Ligands: ACD.18 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:I.419, F:I.419, F:L.595, F:L.595, F:A.598, F:I.599 Hydrogen bonds: F:L.184, F:R.195, F:R.296, F:R.591

6 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.3: 19 residues within 4Å: Chain A: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.358, A:E.362, A:E.362, A:L.367, A:L.367, A:I.405, A:A.409, A:L.413, A:I.419, A:F.420, A:I.599, A:L.603 ACD.6: 19 residues within 4Å: Chain B: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.358, B:E.362, B:E.362, B:L.367, B:L.367, B:I.405, B:A.409, B:L.413, B:I.419, B:F.420, B:I.599, B:L.603 Salt bridges: B:H.602 ACD.9: 19 residues within 4Å: Chain C: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.358, C:E.362, C:E.362, C:L.367, C:L.367, C:I.405, C:A.409, C:L.413, C:I.419, C:F.420, C:I.599, C:L.603 Salt bridges: C:H.602 ACD.12: 19 residues within 4Å: Chain D: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.11 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.358, D:E.362, D:E.362, D:L.367, D:L.367, D:I.405, D:A.409, D:L.413, D:I.419, D:F.420, D:I.599, D:L.603 ACD.15: 19 residues within 4Å: Chain E: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.14 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:F.358, E:E.362, E:E.362, E:L.367, E:L.367, E:I.405, E:A.409, E:L.413, E:I.419, E:F.420, E:I.599, E:L.603 Salt bridges: E:H.602 ACD.18: 19 residues within 4Å: Chain F: F.180, F.358, E.362, H.366, L.367, H.371, I.405, R.408, A.409, L.413, I.419, F.420, Q.553, I.599, S.600, H.602, L.603, I.669 Ligands: ZR5.17 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:F.358, F:E.362, F:E.362, F:L.367, F:L.367, F:I.405, F:A.409, F:L.413, F:I.419, F:F.420, F:I.599, F:L.603 Salt bridges: F:H.602

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mobbs, J.I. et al., Cryo-EM structures of human arachidonate 12S-lipoxygenase bound to endogenous and exogenous inhibitors. Blood (2023)

Release Date

2023-08-09

Peptides

Polyunsaturated fatty acid lipoxygenase ALOX12: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Polyunsaturated fatty acid lipoxygenase ALOX12

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