SMTL ID : 5med.1

Cyanothece lipoxygenase 2 (CspLOX2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.257, H.262, H.449, N.453, I.569 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.257, A:H.262, A:H.449, A:I.569, H2O.3 FE.8: 5 residues within 4Å: Chain B: H.257, H.262, H.449, N.453, I.569 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.257, B:H.262, B:H.449, B:I.569, H2O.24

6 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.2: 8 residues within 4Å: Chain A: V.120, N.162, Y.163, K.164, G.165, C.251, I.255 Ligands: BU1.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.255 Hydrogen bonds: A:Y.163, A:G.165 PGR.10: 4 residues within 4Å: Chain B: L.83, R.103, F.238, I.486 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.83, B:I.486 Hydrogen bonds: B:R.103, B:R.103 PGR.11: 9 residues within 4Å: Chain B: R.57, L.299, Q.303, L.304, Y.310, L.502, T.505, L.506 Ligands: POL.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.299 Hydrogen bonds: B:R.57, B:R.57, B:T.505 Water bridges: B:Y.310 PGR.12: 5 residues within 4Å: Chain B: A.341, R.344, W.377, E.381, A.436 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.341 Hydrogen bonds: B:E.381 Water bridges: B:A.436, B:A.436 PGR.13: 2 residues within 4Å: Chain B: P.231, R.232 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.231 PGR.16: 9 residues within 4Å: Chain A: T.68, L.69, A.70, S.71, I.73 Chain B: T.68, L.69, S.71, I.73 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.68, B:L.69 Hydrogen bonds: A:L.69, A:S.71, B:S.71, B:S.71

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.3: 5 residues within 4Å: Chain A: P.94, Y.454, Y.457, D.458, C.507 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.458 Water bridges: A:Y.457, A:D.458 BU1.4: 5 residues within 4Å: Chain A: R.260, A.328, A.329, E.332 Ligands: PGR.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.329 Hydrogen bonds: A:R.260, A:R.260 Water bridges: A:E.332 BU1.14: 6 residues within 4Å: Chain B: V.120, N.162, Y.163, K.164, G.165, I.255 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.120 Hydrogen bonds: B:Y.163, B:G.165 BU1.15: 5 residues within 4Å: Chain B: E.520, F.521, Q.527, L.530, Q.534 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.520, B:L.530 Hydrogen bonds: B:F.521, B:Q.534

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: K.287, P.288, Q.291, P.517, D.518 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.518 Water bridges: A:Q.291, A:Q.291, A:T.519

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.6: 10 residues within 4Å: Chain A: R.57, H.262, I.296, L.299, A.300, Q.303, L.304, T.505, L.506, I.569 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.296, A:L.299, A:A.300, A:L.304, A:L.304 Hydrogen bonds: A:R.57, A:R.57, A:T.505 Water bridges: A:T.505, A:I.569

2 x POL: N-PROPANOL(Non-covalent)

POL.7: 4 residues within 4Å: Chain A: P.395, T.430, I.431, E.432 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.431, A:E.432, A:E.432 Hydrogen bonds: A:I.431 POL.17: 8 residues within 4Å: Chain B: H.262, I.296, L.299, A.300, L.304, L.506, I.569 Ligands: PGR.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.296, B:L.299, B:A.300, B:L.304 Hydrogen bonds: B:H.262

1 x 1BO: 1-BUTANOL(Non-covalent)

1BO.9: 2 residues within 4Å: Chain B: P.94, Y.457 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.94, B:Y.457

2 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.18: 4 residues within 4Å: Chain A: Q.45, S.46 Chain B: Q.45, S.46 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.45, A:Q.45 PDO.19: 6 residues within 4Å: Chain B: L.38, I.330, M.334, P.414, G.417, R.418 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.414, B:R.418

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newie, J. et al., Lipoxygenase 2 from Cyanothece sp. controls dioxygen insertion by steric shielding and substrate fixation. Sci Rep (2017)

Release Date

2017-05-31

Peptides

Arachidonate 15-lipoxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arachidonate 15-lipoxygenase

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