SMTL ID : 7wpq.1

Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 3.27 angstron resolution (2 units)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.134 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: V.60, N.77, T.79 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain B: F.133, N.134 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain B: V.60, F.75, N.77, T.79 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain C: D.465, V.466, N.468, T.470 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain C: N.94 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain C: N.384 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain D: D.465, V.466, N.468, T.470 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: Q.89, N.94, C.95 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: N.384, A.387 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain E: N.134 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain E: N.77, T.79 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain F: D.465, V.466, N.468, T.470 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain F: Q.89, N.94 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain F: N.384, A.387, P.388 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: F.133, N.134 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: V.60, N.77, T.79 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain H: D.465, V.466, N.468, T.470 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: Q.89, N.94 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain H: R.382, N.384, P.388 Ligand excluded by PLIP

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

CA.3: 6 residues within 4Å: Chain A: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.25, A:F.146 CA.4: 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.7: 6 residues within 4Å: Chain B: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.25, B:F.146 CA.8: 6 residues within 4Å: Chain B: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.378, B:N.508, B:D.511, B:D.512 CA.12: 6 residues within 4Å: Chain C: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.116, C:D.237, C:I.239, C:D.243 CA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 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.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 6 residues within 4Å: Chain E: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.25, E:F.146 CA.22: 6 residues within 4Å: Chain E: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.378, E:N.508, E:D.511, E:D.512 CA.26: 6 residues within 4Å: Chain F: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.116, F:D.237, F:I.239, F:D.243 CA.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.30: 6 residues within 4Å: Chain G: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.25, G:F.146 CA.31: 6 residues within 4Å: Chain G: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.378, G:N.508, G:D.511, G:D.512 CA.35: 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.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, J. et al., Structural basis of von Willebrand factor multimerization and tubular storage. Blood (2022)

Release Date

2022-05-25

Peptides

von Willebrand antigen 2: ABEG
von Willebrand factor: CDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

G
G

C
C

D
D

F
F

H
H

von Willebrand antigen 2

von Willebrand factor

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