SMTL ID : 6zbr.1

VEGF-A 13:107 crystallized with 4C bicyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-2-mer

Ligands

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

MPD.1: 5 residues within 4Å: Chain A: W.9 Chain B: M.69, Q.77, H.78, I.79 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.77, B:I.79 MPD.2: 5 residues within 4Å: Chain B: Q.67, I.79, G.80, E.81 Chain C: V.2 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.79 Hydrogen bonds: B:Q.67, B:E.81, B:E.81 MPD.3: 9 residues within 4Å: Chain B: E.18, P.41, L.42, M.43, I.64, M.66, Q.86 Chain C: V.3, R.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.64, C:V.3 Hydrogen bonds: B:Q.86, B:Q.86, C:R.11 MPD.4: 4 residues within 4Å: Chain C: Q.67, I.79, G.80, E.81 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.67, C:Q.67, C:Q.67 MPD.5: 3 residues within 4Å: Chain C: E.30, Y.33, R.70 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.30, C:R.70

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

PO4.6: 4 residues within 4Å: Chain C: E.61, S.62, N.63, L.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.63, C:N.63

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

2021-06-23

Peptides

Chains: P: A
Vascular endothelial growth factor A: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
V

C
W

Chains: P

Vascular endothelial growth factor A

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