SMTL ID : 7wn3.1

Cryo-EM structure of VWF D'D3 dimer (2M mutant) complexed with D1D2 at 3.29 angstron resolution (2 units)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.29 Å

Oligo State

hetero-4-4-mer

Ligands

16 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 5 residues within 4Å: Chain A: D.25, N.142, N.144, F.146, D.150 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.25, A:N.142 CA.2: 6 residues within 4Å: Chain A: D.378, N.504, N.506, N.508, D.511, D.512 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.378, A:D.511, A:D.512 CA.6: 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.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain C: D.25, N.142, N.144, F.146, D.150 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.25, C:N.142 CA.11: 6 residues within 4Å: Chain C: D.378, N.504, N.506, N.508, D.511, D.512 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.378, C:D.511, C:D.512 CA.15: 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 CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.19: 5 residues within 4Å: Chain E: D.25, N.142, N.144, F.146, D.150 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.25, E:N.142 CA.20: 6 residues within 4Å: Chain E: D.378, N.504, N.506, N.508, D.511, D.512 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.378, E:D.511, E:D.512 CA.23: 5 residues within 4Å: Chain F: D.25, N.142, N.144, F.146, D.150 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.25, F:N.142 CA.24: 6 residues within 4Å: Chain F: D.378, N.504, N.506, N.508, D.511, D.512 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.378, F:D.511, F:D.512 CA.28: 6 residues within 4Å: Chain G: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.116, G:D.237, G:I.239, G:D.243 CA.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.33: 6 residues within 4Å: Chain H: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.116, H:D.237, H:I.239, H:D.243 CA.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.134 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: V.60, N.77, T.79 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain B: D.465, V.466, N.468, T.470, E.472 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain B: Q.89, N.94 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: R.382, Y.383, N.384 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain C: N.134 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain C: N.77, T.79 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain D: D.465, V.466, N.468, T.470, E.472 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: Q.89, N.94 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: N.384, P.388 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain E: N.134 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain E: F.75, V.76, N.77, T.79, R.86 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain F: N.134 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain F: V.60, F.75, N.77 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain G: D.465, V.466, N.468, T.470, E.472 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain G: Q.89, N.94, C.95, T.96 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: R.382, N.384, A.387, H.413 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain H: D.465, V.466, N.468, T.470, E.472 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain H: Q.89, W.93, N.94 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: L.372 Chain H: R.382, N.384 Ligand excluded by 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

2022-05-25

Peptides

von Willebrand antigen 2: ACEF
von Willebrand factor: BDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
E

F
G

B
F

D
H

G
C

H
D

von Willebrand antigen 2

von Willebrand factor

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