SMTL ID : 2x1x.1

CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-mer

Ligands

4 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: 7 residues within 4Å: Chain A: N.64, T.65, S.66, T.67, Y.69, A.93, H.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.69 NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: Y.49, L.70, N.94, H.95, T.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.49 NAG-NAG-BMA.7: 7 residues within 4Å: Chain C: N.64, T.65, S.66, T.67, Y.69, A.93, H.95 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.69 NAG-NAG-BMA.8: 5 residues within 4Å: Chain C: Y.49, L.70, N.94, H.95, T.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.49

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.3: 6 residues within 4Å: Chain B: S.110, P.111, V.124, N.126, R.156, L.170 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: V.107, K.198, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain D: S.110, P.111, V.124, N.126, R.156, L.170 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: V.107, K.198, N.199 No protein-ligand interaction detected (PLIP)

2 x HG: MERCURY (II) ION(Non-covalent)

HG.5: 2 residues within 4Å: Chain B: C.43, R.50 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.43, H2O.1 HG.11: 2 residues within 4Å: Chain D: C.43, R.50 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.43, H2O.1

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

NAG.6: 1 residues within 4Å: Chain B: N.24 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain D: N.24 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leppanen, V.-M. et al., Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-02-09

Peptides

VASCULAR ENDOTHELIAL GROWTH FACTOR C: AC
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
E

B
R

D
R

VASCULAR ENDOTHELIAL GROWTH FACTOR C

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2

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