SMTL ID : 3ala.4 (3 other biounits)

Crystal structure of vascular adhesion protein-1 in space group C2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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(Non-covalent)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: F.115, Q.118, N.122, S.124, V.142, P.148 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 9 residues within 4Å: Chain B: L.64, F.115, Q.118, N.122, S.124, M.137, D.139, T.141, P.148 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.64, B:F.115

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.2: 6 residues within 4Å: Chain A: R.191, N.217, S.219 Chain B: Y.433, S.434, D.713 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: Y.433, S.434, H.435, R.711, D.713 Chain B: R.191, N.217, S.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.435, A:D.713, A:D.713

1 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.3: 3 residues within 4Å: Chain A: E.521, N.577, H.578 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.578

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.6: 2 residues within 4Å: Chain B: W.523, N.577 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.577

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

CU.7: 3 residues within 4Å: Chain A: H.505, H.507, H.669 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.505, A:H.507, A:H.669 CU.10: 3 residues within 4Å: Chain B: H.505, H.507, H.669 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.505, B:H.507, B:H.669

4 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: K.91, D.514, L.515, D.516, D.658, L.659 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.514, A:L.515, A:D.516, A:D.658, A:L.659 CA.9: 5 residues within 4Å: Chain A: K.623, E.626, F.648, N.650, E.652 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.626 CA.11: 7 residues within 4Å: Chain B: K.91, D.514, L.515, D.516, L.520, D.658, L.659 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.514, B:L.515, B:D.516, B:D.658, B:L.659 CA.12: 6 residues within 4Å: Chain B: E.557, K.623, E.626, F.648, N.650, E.652 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.557, B:F.648, B:E.652

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ernberg, K. et al., A new crystal form of human vascular adhesion protein 1. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-12-15

Peptides

Membrane primary amine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

Membrane primary amine oxidase

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