SMTL ID : 1rky.1

PPLO + Xe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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(Post Translational Modification)

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.64, E.67, 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.27: 5 residues within 4Å: Chain B: N.64, E.67, 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

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

NAG.2: 2 residues within 4Å: Chain A: N.41, T.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Water bridges: A:N.53 NAG.3: 3 residues within 4Å: Chain A: N.147, N.151, R.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.147, A:N.151, A:R.156 NAG.4: 3 residues within 4Å: Chain A: D.262, N.269, S.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.262 Hydrogen bonds: A:D.262, A:N.269 NAG.5: 3 residues within 4Å: Chain A: K.26, T.383, N.394 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.26 Hydrogen bonds: A:N.394 NAG.28: 2 residues within 4Å: Chain B: N.41, T.43 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.41, B:T.43 Water bridges: B:N.53 NAG.29: 3 residues within 4Å: Chain B: N.147, N.151, R.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.147, B:N.151, B:R.156 NAG.30: 3 residues within 4Å: Chain B: D.262, N.269, S.271 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.262 Hydrogen bonds: B:D.262, B:D.262, B:N.269 NAG.31: 3 residues within 4Å: Chain B: K.26, T.383, N.394 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.26 Hydrogen bonds: B:N.394

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

CU.6: 4 residues within 4Å: Chain A: Y.438, H.488, H.490, H.654 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.488, A:H.490, A:H.654 CU.32: 4 residues within 4Å: Chain B: Y.438, H.488, H.490, H.654 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.488, B:H.490, B:H.654

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.18 CA.8: 4 residues within 4Å: Chain A: E.540, 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.14, H2O.24 CA.33: 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.42 CA.34: 4 residues within 4Å: Chain B: E.540, 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.38, H2O.48

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

MG.9: 1 residues within 4Å: Chain A: S.23 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain A: D.296 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain B: S.23 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Chain B: D.296 No protein-ligand interaction detected (PLIP)

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

CL.12: 4 residues within 4Å: Chain A: A.622, L.623, Y.624, D.625 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: K.124, S.125, K.126 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: I.256, D.257, D.481 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: A.533, R.534 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: G.380, Y.381 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: F.51, D.219 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain B: A.622, L.623, Y.624, D.625 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain B: K.124, S.125, K.126 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: I.256, D.257, D.481 Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain B: A.533, R.534 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain B: G.380, Y.381 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain B: F.51, D.219 Ligand excluded by PLIP

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.18: 6 residues within 4Å: Chain A: Y.356, D.358, Y.361, I.435, N.437, Y.438 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.356 pi-Stacking: A:Y.356, A:Y.361 IMD.44: 6 residues within 4Å: Chain B: Y.356, D.358, Y.361, I.435, N.437, Y.438 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:Y.356, B:Y.361

16 x XE: XENON(Non-covalent)

XE.19: 4 residues within 4Å: Chain A: W.307, I.331, V.332, Y.572 Ligand excluded by PLIP XE.20: 6 residues within 4Å: Chain A: M.225, L.226, E.227, Y.228, T.236, S.237 Ligand excluded by PLIP XE.21: 3 residues within 4Å: Chain A: A.669 Ligands: XE.25, XE.26 Ligand excluded by PLIP XE.22: 4 residues within 4Å: Chain A: Y.373, D.374 Chain B: D.407, Y.408 Ligand excluded by PLIP XE.23: 2 residues within 4Å: Chain A: Q.509, P.548 Ligand excluded by PLIP XE.24: 3 residues within 4Å: Chain A: K.26, V.29, Q.30 Ligand excluded by PLIP XE.25: 7 residues within 4Å: Chain A: V.456, H.490, L.492, L.650, G.651 Ligands: XE.21, XE.26 Ligand excluded by PLIP XE.26: 5 residues within 4Å: Chain A: A.458, H.490, L.492 Ligands: XE.21, XE.25 Ligand excluded by PLIP XE.45: 4 residues within 4Å: Chain B: W.307, I.331, V.332, Y.572 Ligand excluded by PLIP XE.46: 6 residues within 4Å: Chain B: M.225, L.226, E.227, Y.228, T.236, S.237 Ligand excluded by PLIP XE.47: 3 residues within 4Å: Chain B: A.669 Ligands: XE.51, XE.52 Ligand excluded by PLIP XE.48: 4 residues within 4Å: Chain A: D.407, Y.408 Chain B: Y.373, D.374 Ligand excluded by PLIP XE.49: 2 residues within 4Å: Chain B: Q.509, P.548 Ligand excluded by PLIP XE.50: 3 residues within 4Å: Chain B: K.26, V.29, Q.30 Ligand excluded by PLIP XE.51: 7 residues within 4Å: Chain B: V.456, H.490, L.492, L.650, G.651 Ligands: XE.47, XE.52 Ligand excluded by PLIP XE.52: 5 residues within 4Å: Chain B: A.458, H.490, L.492 Ligands: XE.47, XE.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duff, A.P. et al., Using Xenon as a Probe for Dioxygen-binding Sites in Copper Amine Oxidases. J.Mol.Biol. (2004)

Release Date

2004-12-07

Peptides

lysyl oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

lysyl oxidase

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