SMTL ID : 6zfl.1

High resolution structure of VEGF-A 12:107 crystallized in tetragonal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 4 residues within 4Å: Chain A: E.62, S.63, N.64, L.86 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.62 Hydrogen bonds: A:N.64 MPD.2: 7 residues within 4Å: Chain A: C.46, G.47, G.48 Chain B: L.21, V.22, D.23, C.40 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.48, B:L.21 Water bridges: B:D.23 MPD.4: 7 residues within 4Å: Chain A: L.21, V.22, D.23, C.40 Chain B: C.46, G.47, G.48 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.48, A:L.21 Hydrophobic interactions: A:D.23 MPD.5: 4 residues within 4Å: Chain B: E.62, S.63, N.64, L.86 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.62 Hydrogen bonds: B:N.64

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 1 residues within 4Å: Chain A: M.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.1 Water bridges: A:M.1 PO4.6: 1 residues within 4Å: Chain B: M.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.1, B:M.1 PO4.7: 4 residues within 4Å: Chain B: Y.34, R.71, Q.76, H.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.34, B:Y.34, B:Q.76 Salt bridges: B:R.71, B:H.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaucher, J.F. et al., Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands. Chemistry (2022)

Release Date

2021-06-30

Peptides

Vascular endothelial growth factor A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
W

Vascular endothelial growth factor A