SMTL ID : 2c10.2 (1 other biounit)

The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

1 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: 8 residues within 4Å: Chain A: F.102, Q.105, N.109, S.111, M.124, D.126, V.129, P.135 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.126

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 1 residues within 4Å: Chain A: N.564 No protein-ligand interaction detected (PLIP)

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.3: 7 residues within 4Å: Chain A: V.181, N.204, S.206 Chain B: Y.420, S.421, H.422, D.700 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.422 NAG-NAG.6: 9 residues within 4Å: Chain A: Y.420, S.421, H.422, R.698, D.700 Chain B: R.178, V.181, N.204, S.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.422

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.4: 5 residues within 4Å: Chain B: F.102, Q.105, N.109, S.111, V.129 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.5: 2 residues within 4Å: Chain B: N.564 Ligands: NAG.15 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.266 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain B: N.266 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain B: N.638 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-FUC.5, NAG-NAG-BMA-MAN-FUC.5 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: K.78, D.501, L.502, D.503, D.645, L.646 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.501, A:L.502, A:D.503, A:D.645, A:L.646, H2O.5 CA.10: 4 residues within 4Å: Chain A: E.544, F.635, N.637, E.639 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.544, A:E.544, A:F.635, A:E.639 CA.16: 6 residues within 4Å: Chain B: K.78, D.501, L.502, D.503, D.645, L.646 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.501, B:L.502, B:D.503, B:D.645, B:L.646, H2O.9 CA.18: 4 residues within 4Å: Chain B: E.544, F.635, N.637, E.639 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.544, B:F.635, B:E.639, H2O.10, H2O.10

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

CU.9: 3 residues within 4Å: Chain A: H.492, H.494, H.656 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.492, A:H.494, A:H.656, H2O.3 CU.17: 3 residues within 4Å: Chain B: H.492, H.494, H.656 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.492, B:H.494, B:H.656, H2O.9

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

CL.11: 4 residues within 4Å: Chain A: R.355, S.591 Chain B: L.531, Q.532 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: Y.138, H.139, K.224 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: L.531, Q.532 Chain B: R.355 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: Y.138, H.139, K.224 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jakobsson, E. et al., Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1. Acta Crystallogr. D Biol. Crystallogr. (2005)

Release Date

2006-09-20

Peptides

MEMBRANE COPPER AMINE OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

MEMBRANE COPPER AMINE OXIDASE

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