SMTL ID : 6z3f.1

VEGF-A 13:107 crystallized with 2C bicyclic peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-2-mer

Ligands

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

NH2.1: 1 residues within 4Å: Chain A: K.14 No protein-ligand interaction detected (PLIP)

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

MPD.2: 7 residues within 4Å: Chain A: W.9, F.12, E.13 Chain B: M.69, Q.77, H.78, I.79 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.77

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

ACY.3: 1 residues within 4Å: Chain B: H.74 No protein-ligand interaction detected (PLIP) ACY.4: 3 residues within 4Å: Chain B: Q.67, I.79, E.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.67, B:E.81 ACY.5: 7 residues within 4Å: Chain B: E.18, P.41, L.42, M.43, I.64, M.66, Q.86 No protein-ligand interaction detected (PLIP) ACY.6: 2 residues within 4Å: Chain C: S.62, N.63 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.63 ACY.7: 4 residues within 4Å: Chain C: Q.67, I.79, G.80, E.81 No protein-ligand interaction detected (PLIP)

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

2021-06-02

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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