SMTL ID : 6z13.1

VEGF-A 13:107 crystallized with 3C bicyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-2-mer

Ligands

1 x NH2: AMINO GROUP(Non-functional Binders)

NH2.1: 4 residues within 4Å: Chain A: E.13, K.14, L.15 Chain B: Q.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.77

5 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 3 residues within 4Å: Chain B: E.1, V.2 Chain C: T.65 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.1 ACY.3: 8 residues within 4Å: Chain B: E.18, P.41, L.42, M.43, I.64, M.66, Q.86 Chain C: R.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.11 Hydrophobic interactions: B:E.18 Hydrogen bonds: B:Q.86 ACY.4: 5 residues within 4Å: Chain A: W.9 Chain B: M.69, Q.77, H.78, I.79 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.77 Hydrogen bonds: B:Q.77, B:I.79 ACY.6: 2 residues within 4Å: Chain C: Q.77, I.79 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.77 ACY.7: 4 residues within 4Å: Chain C: Q.67, I.79, G.80, E.81 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.67 Water bridges: B:K.4

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

MPD.5: 6 residues within 4Å: Chain B: Q.67, I.79, G.80, E.81 Chain C: V.2, K.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.67, B:E.81 MPD.8: 9 residues within 4Å: Chain B: V.3, R.11 Chain C: E.18, P.41, L.42, M.43, I.64, M.66, Q.86 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:E.18, C:P.41, C:I.64, B:V.3 Hydrogen bonds: C:P.41

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

2021-05-26

Peptides

bicyclic peptide 3C: A
Vascular endothelial growth factor A: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
V

C
W

bicyclic peptide 3C

Vascular endothelial growth factor A

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