SMTL ID : 1w7c.1

PPLO at 1.23 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 10 residues within 4Å: Chain A: P.63, N.64, E.67, P.80, N.82, K.101, E.114, F.118, D.609, T.610 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.610 Hydrogen bonds: A:K.101, A:K.101 NAG-NAG-BMA.20: 10 residues within 4Å: Chain B: P.63, N.64, E.67, P.80, N.82, K.101, E.114, F.118, D.609, T.610 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.610 Hydrogen bonds: B:K.101, B:K.101

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

CU.2: 4 residues within 4Å: Chain A: Y.438, H.488, H.490, H.654 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.488, A:H.490, A:H.654, H2O.40 CU.21: 4 residues within 4Å: Chain B: Y.438, H.488, H.490, H.654 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.488, B:H.490, B:H.654, H2O.81

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: K.65, D.497, L.498, D.499, D.643, I.644 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.497, A:L.498, A:D.499, A:D.643, A:I.644, H2O.29 CA.4: 6 residues within 4Å: Chain A: E.540, K.606, K.608, F.633, D.635, E.637 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.540, A:F.633, A:E.637, H2O.35, H2O.35 CA.22: 6 residues within 4Å: Chain B: K.65, D.497, L.498, D.499, D.643, I.644 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.497, B:L.498, B:D.499, B:D.643, B:I.644, H2O.69 CA.23: 6 residues within 4Å: Chain B: E.540, K.606, K.608, F.633, D.635, E.637 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.540, B:F.633, B:E.637, H2O.75, H2O.75

10 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: S.23, A.25 No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain A: D.298, E.299 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: P.104, E.110 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: H.607 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain B: S.23, A.25 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain B: D.298, E.299 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain B: P.104, E.110 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain B: H.607 No protein-ligand interaction detected (PLIP)

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 7 residues within 4Å: Chain A: V.131, H.180, P.182, A.622, L.623, Y.624, D.625 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.124, S.125, K.126 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: I.256, D.257, H.480, D.481, V.482 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: A.533, R.534 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: G.380, Y.381 Ligand excluded by PLIP CL.29: 7 residues within 4Å: Chain B: V.131, H.180, P.182, A.622, L.623, Y.624, D.625 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: K.124, S.125, K.126 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: I.256, D.257, H.480, D.481, V.482 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: A.533, R.534 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: G.380, Y.381 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.15: 8 residues within 4Å: Chain A: Y.356, D.358, Y.361, I.435, G.436, N.437, Y.438, Y.440 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.358, A:N.437 Water bridges: A:Y.356 pi-Stacking: A:Y.356, A:Y.361 IMD.34: 8 residues within 4Å: Chain B: Y.356, D.358, Y.361, I.435, G.436, N.437, Y.438, Y.440 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.358, B:N.437 pi-Stacking: B:Y.356, B:Y.361

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

NAG.16: 2 residues within 4Å: Chain A: N.41, T.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:N.41, A:N.41, A:T.43 NAG.17: 5 residues within 4Å: Chain A: N.147, N.151, R.156, Y.167, E.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.147, A:N.151, A:R.156 Water bridges: A:E.168 NAG.18: 4 residues within 4Å: Chain A: D.262, V.265, N.269, S.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.262 Hydrogen bonds: A:N.269 NAG.19: 6 residues within 4Å: Chain A: K.26, T.383, F.392, N.394, T.396, I.736 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.26 Hydrogen bonds: A:N.394 Water bridges: A:N.394 NAG.35: 2 residues within 4Å: Chain B: N.41, T.43 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.41, B:T.43 Water bridges: B:N.41, B:N.41, B:T.43 NAG.36: 5 residues within 4Å: Chain B: N.147, N.151, R.156, Y.167, E.168 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.147, B:N.151, B:R.156 Water bridges: B:E.168, B:E.168 NAG.37: 4 residues within 4Å: Chain B: D.262, V.265, N.269, S.271 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.262 Hydrogen bonds: B:D.262, B:N.269, B:S.271 NAG.38: 6 residues within 4Å: Chain B: K.26, T.383, F.392, N.394, T.396, I.736 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.26 Hydrogen bonds: B:N.394 Water bridges: B:N.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duff, A.P. et al., The 1.23 A Structure of Pichia Pastoris Lysyl Oxidase Reveals a Lysine-Lysine Cross-Link. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-08-31

Peptides

LYSYL OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

LYSYL OXIDASE

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