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

Crystal structure of vascular apoptosis-inducing protein-1(inhibitor-bound form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

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.1: 4 residues within 4Å: Chain A: N.35, T.37, A.38, T.41 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.35, A.38 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.152, H.156, H.162 Ligands: GM6.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.152, A:H.156, A:H.162 ZN.8: 4 residues within 4Å: Chain B: H.152, H.156, H.162 Ligands: GM6.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.152, B:H.156, B:H.162

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.232, A:E.232, A:D.235 CA.4: 5 residues within 4Å: Chain A: D.286, M.287, D.289, D.300, R.301 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.286, A:M.287, A:D.289, A:D.300, A:R.301 CA.9: 7 residues within 4Å: Chain B: V.222, C.223, 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.10: 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.289, B:R.301

1 x 3CO: COBALT (III) ION(Non-covalent)

3CO.5: 3 residues within 4Å: Chain A: K.15, H.55, H.60 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.55, A:H.60

2 x GM6: 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE(Non-covalent)

GM6.6: 15 residues within 4Å: Chain A: P.116, T.117, A.118, G.119, L.120, A.149, H.152, E.153, H.156, H.162, A.177, G.178, A.179, L.180 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.116, A:P.116, A:A.149, A:L.180, A:L.180 Hydrogen bonds: A:P.116, A:A.118, A:G.178, A:L.180 GM6.11: 15 residues within 4Å: Chain B: P.116, T.117, A.118, G.119, L.120, A.149, H.152, E.153, H.156, H.162, A.177, G.178, A.179, L.180 Ligands: ZN.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.116, B:P.116, B:A.149, B:L.180 Hydrogen bonds: B:P.116, B:A.118, B:G.178, B:L.180

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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