SMTL ID : 1n9e.2 (1 other biounit)

Crystal structure of Pichia pastoris Lysyl Oxidase PPLO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.104, E.107, N.122, F.158, D.649, E.650 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: N.104, E.107, N.122, E.154, F.158, D.649 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.141, B:E.154

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: N.81, F.91, S.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.91 Water bridges: A:N.93, A:N.93 NAG.4: 4 residues within 4Å: Chain A: N.187, N.191, R.196, E.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.187, A:N.191, A:R.196 Water bridges: A:E.208 NAG.5: 3 residues within 4Å: Chain A: D.302, N.309, S.311 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.302 Hydrogen bonds: A:D.302, A:D.302 NAG.6: 4 residues within 4Å: Chain A: K.66, T.423, N.434, T.436 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.66 Water bridges: A:N.434 NAG.17: 2 residues within 4Å: Chain B: N.81, T.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.83 Water bridges: B:N.81, B:N.81, B:S.92 NAG.18: 3 residues within 4Å: Chain B: N.187, N.191, R.196 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.187, B:N.191, B:R.196 Water bridges: B:E.208 NAG.19: 3 residues within 4Å: Chain B: D.302, N.309, S.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.302, B:N.309, B:S.311 NAG.20: 3 residues within 4Å: Chain B: T.423, N.434, T.436 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.423, B:N.434

2 x CU: COPPER (II) ION(Non-covalent)

CU.7: 4 residues within 4Å: Chain A: Y.478, H.528, H.530, H.694 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.528, A:H.530, A:H.694 CU.21: 4 residues within 4Å: Chain B: Y.478, H.528, H.530, H.694 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.528, B:H.530, B:H.694

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: K.105, D.537, L.538, D.539, D.683, I.684 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.537, A:L.538, A:D.539, A:D.683, A:I.684, H2O.2 CA.9: 4 residues within 4Å: Chain A: E.580, F.673, D.675, E.677 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.673, A:D.675, A:E.677, H2O.3, H2O.4 CA.22: 6 residues within 4Å: Chain B: K.105, D.537, L.538, D.539, D.683, I.684 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.537, B:L.538, B:D.539, B:D.683, B:I.684, H2O.44 CA.23: 4 residues within 4Å: Chain B: E.580, F.673, D.675, E.677 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.580, B:F.673, B:E.677, H2O.46, H2O.46

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 6 residues within 4Å: Chain A: L.483, K.485, E.493, R.497 Chain B: D.447, Y.448 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.493 Water bridges: A:K.485, A:K.485, A:R.497, A:R.497, A:R.497 Salt bridges: A:K.485, A:R.497 SO4.11: 7 residues within 4Å: Chain A: V.171, H.220, P.222, A.662, L.663, Y.664, D.665 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.661, A:Y.664, A:Y.664, A:D.665 Water bridges: A:L.663, A:L.663 SO4.12: 4 residues within 4Å: Chain A: R.176, N.405, Y.429, R.772 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.405 Water bridges: A:R.176, A:R.176, A:R.176, A:R.355, A:R.406, A:Y.429, A:R.772 Salt bridges: A:R.176, A:R.772 SO4.13: 4 residues within 4Å: Chain A: F.721, D.722, S.723, N.725 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.722, A:S.723, A:S.723, A:N.725 Water bridges: A:S.723, A:S.723 SO4.14: 4 residues within 4Å: Chain A: N.300, L.301, D.302, W.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.302, A:D.302, A:W.303 SO4.15: 3 residues within 4Å: Chain A: K.164, S.165, K.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.165, A:S.165, A:K.166 Salt bridges: A:K.166 SO4.16: 3 residues within 4Å: Chain A: N.50, R.331, Y.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.50, A:Y.335, A:Y.335 Water bridges: A:R.331 Salt bridges: A:R.331 SO4.24: 6 residues within 4Å: Chain A: D.447, Y.448 Chain B: L.483, K.485, E.493, R.497 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:R.470, B:K.485, B:K.485, A:E.446 Salt bridges: B:K.485, B:R.497 Hydrogen bonds: A:D.447 SO4.25: 8 residues within 4Å: Chain B: V.171, H.220, P.222, N.661, A.662, L.663, Y.664, D.665 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.661, B:Y.664, B:D.665 Water bridges: B:L.663, B:L.663 SO4.26: 4 residues within 4Å: Chain B: R.176, N.405, Y.429, R.772 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.405 Water bridges: B:R.176, B:R.176, B:R.355, B:R.406, B:Y.429, B:R.772 Salt bridges: B:R.176, B:R.772 SO4.27: 4 residues within 4Å: Chain B: F.721, D.722, S.723, N.725 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.722, B:S.723, B:S.723, B:N.725 Water bridges: B:D.722, B:D.722, B:S.723, B:S.723 SO4.28: 4 residues within 4Å: Chain B: N.300, L.301, D.302, W.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.302, B:D.302, B:W.303 SO4.29: 3 residues within 4Å: Chain B: K.164, S.165, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.165, B:S.165, B:K.166 Salt bridges: B:K.166 SO4.30: 3 residues within 4Å: Chain B: N.50, R.331, Y.335 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.335 Water bridges: B:N.50, B:R.331, B:R.331 Salt bridges: B:R.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duff, A.P. et al., The Crystal Structure of Pichia pastoris Lysyl Oxidase. Biochemistry (2003)

Release Date

2004-01-13

Peptides

LYSYL OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

LYSYL OXIDASE

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