SMTL ID : 5oyj.1

Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-2-2-mer

Ligands

7 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: 8 residues within 4Å: Chain C: I.48, P.49, L.50, E.51, N.53, H.54, I.56, R.70 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.48, C:L.50 NAG-NAG.2: 4 residues within 4Å: Chain A: F.145 Chain C: N.46, N.74 Ligands: NA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: E.130 Chain C: F.183, L.185, N.190 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.183 NAG-NAG.4: 4 residues within 4Å: Chain C: F.170, K.175, N.202, V.203 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.175 NAG-NAG.5: 7 residues within 4Å: Chain D: L.50, E.51, N.53, H.54, T.55, I.56, R.70 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: G.73, N.74 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: P.131, F.183, N.190 No protein-ligand interaction detected (PLIP)

3 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.8: 3 residues within 4Å: Chain B: Y.57, G.58, H.92 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.92 GLC-GLC.9: 3 residues within 4Å: Chain C: R.26, V.27, R.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.28 GLC-GLC.10: 2 residues within 4Å: Chain D: Q.171, G.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.171

4 x CA: CALCIUM ION(Non-covalent)

CA.11: 2 residues within 4Å: Chain A: G.25, D.27 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.25, A:D.27, H2O.3 CA.12: 1 residues within 4Å: Chain A: L.100 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.100, H2O.1, H2O.3, H2O.3 CA.13: 2 residues within 4Å: Chain A: D.160 Chain D: E.5 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:D.160, D:E.5, H2O.8 CA.15: 3 residues within 4Å: Chain A: G.157, E.159 Chain C: Q.88 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 3 residues within 4Å: Chain A: Q.142, G.146 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP)

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.16: 2 residues within 4Å: Chain C: E.143, S.204 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.204 Water bridges: C:E.143, C:S.204

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.17: 4 residues within 4Å: Chain C: E.142, C.145, A.146, N.147 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thieltges, K.M. et al., Characterization of a drug-targetable allosteric site regulating vascular endothelial growth factor signaling. Angiogenesis (2018)

Release Date

2018-03-14

Peptides

DARPin D4b: AB
Vascular endothelial growth factor receptor 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DARPin D4b

Vascular endothelial growth factor receptor 2