SMTL ID : 7wn4.1

Cryo-EM structure of VWF D'D3 dimer (wild type) complexed with D1D2 at 3.4 angstron resolution (1 unit)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-2-2-mer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.25, N.142, N.144, F.146, D.149, D.150 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.146, A:D.149, A:D.150 CA.2: 6 residues within 4Å: Chain A: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.378, A:N.508, A:D.511, A:D.512 CA.5: 6 residues within 4Å: Chain B: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.116, B:D.237, B:I.239, B:D.243 CA.8: 6 residues within 4Å: Chain C: D.25, N.142, N.144, F.146, D.149, D.150 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.25, C:F.146, C:D.149, C:D.150 CA.9: 6 residues within 4Å: Chain C: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.378, C:N.508, C:D.511, C:D.512 CA.12: 6 residues within 4Å: Chain D: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.116, D:D.237, D:I.239, D:D.243

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: F.75, N.77, T.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.79, A:T.79 NAG.4: 1 residues within 4Å: Chain A: N.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.134 NAG.6: 1 residues within 4Å: Chain B: N.94 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain B: N.384, A.387, P.388, H.413 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain C: N.77, T.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.77 NAG.11: 2 residues within 4Å: Chain C: F.133, N.134 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.133 Hydrogen bonds: C:N.134 NAG.13: 2 residues within 4Å: Chain D: Q.89, N.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.89, D:N.94 NAG.14: 1 residues within 4Å: Chain D: N.384 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shu, Z. et al., Structural mechanism of VWF D'D3 dimer formation. Cell Discov (2022)

Release Date

2022-05-18

Peptides

von Willebrand antigen 2: AC
von Willebrand factor: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

von Willebrand antigen 2

von Willebrand factor

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