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

Crystal structure of vascular apoptosis-inducing protein-1(tetragonal crystal form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

1 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: 4 residues within 4Å: Chain A: N.35, T.37, A.38, T.41 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.152, H.156, H.162 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.152, A:H.156, A:H.162 ZN.6: 3 residues within 4Å: Chain B: H.152, H.156, H.162 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.152, B:H.156, B:H.162, H2O.7, H2O.7

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: V.222, N.225, F.227, E.229, E.232, D.235 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.222, A:F.227, A:E.229, A:E.232, A:D.235 CA.4: 5 residues within 4Å: Chain A: D.286, M.287, D.289, D.300, R.301 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.286, A:M.287, A:D.289, A:D.300, A:R.301, H2O.4 CA.7: 6 residues within 4Å: Chain B: V.222, N.225, F.227, E.229, E.232, D.235 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:V.222, B:F.227, B:E.229, B:E.232, B:D.235 CA.8: 5 residues within 4Å: Chain B: D.286, M.287, D.289, D.300, R.301 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.286, B:M.287, B:D.289, B:D.300, B:R.301

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

NAG.5: 3 residues within 4Å: Chain B: N.35, T.37, A.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeda, S. et al., Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold. Embo J. (2006)

Release Date

2006-06-20

Peptides

vascular apoptosis-inducing protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

vascular apoptosis-inducing protein 1

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