SMTL ID : 7wps.1

Cryo-EM structure of VWF D'D3 dimer complexed with D1D2 at 4.3 angstron resolution (7 units)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-mer

Ligands

42 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: 5 residues within 4Å: Chain A: Q.55, V.60, F.75, N.77, T.79 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain B: Q.89, N.94 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain C: F.133, N.134 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain C: Q.55, V.60, N.77, T.79 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain E: F.133, N.134 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain E: F.75, N.77, T.79 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain F: F.133, N.134 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain F: F.75, N.77, T.79 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain G: F.133, N.134 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain G: F.75, N.77, T.79 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain H: F.133, N.134 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain H: F.75, N.77, T.79 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain K: F.133, N.134 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain K: F.75, N.77, T.79 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain L: F.133, N.134 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain L: F.75, N.77, T.79 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain M: N.134 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain M: F.75, N.77 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain N: N.134, D.149 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain N: N.77, T.79 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain P: F.133, N.134 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain P: N.77 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain Q: Q.89, N.94 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain Q: R.382, N.384, A.387, P.388 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain R: N.94, C.95 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain S: Q.89, N.94 Ligand excluded by PLIP NAG.64: 5 residues within 4Å: Chain S: R.382, N.384, C.386, A.387, P.388 Ligand excluded by PLIP NAG.65: 6 residues within 4Å: Chain S: H.463, D.465, V.466, N.468, T.470, E.472 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain T: Q.89, N.94 Ligand excluded by PLIP NAG.69: 4 residues within 4Å: Chain T: N.384, C.386, A.387, P.388 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain U: N.94, C.95 Ligand excluded by PLIP NAG.73: 4 residues within 4Å: Chain U: N.384, C.386, A.387, P.388 Ligand excluded by PLIP NAG.76: 1 residues within 4Å: Chain V: N.94 Ligand excluded by PLIP NAG.77: 2 residues within 4Å: Chain V: N.384, H.413 Ligand excluded by PLIP NAG.84: 2 residues within 4Å: Chain Y: Q.89, N.94 Ligand excluded by PLIP NAG.85: 2 residues within 4Å: Chain Y: N.384, P.388 Ligand excluded by PLIP NAG.88: 1 residues within 4Å: Chain Z: N.94 Ligand excluded by PLIP NAG.91: 1 residues within 4Å: Chain 0: N.94 Ligand excluded by PLIP NAG.92: 3 residues within 4Å: Chain 0: N.384, A.387, P.388 Ligand excluded by PLIP NAG.95: 2 residues within 4Å: Chain 1: Q.89, N.94 Ligand excluded by PLIP NAG.96: 3 residues within 4Å: Chain 1: R.382, N.384, P.388 Ligand excluded by PLIP

56 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.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: 6 residues within 4Å: Chain C: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.25, C:F.146 CA.11: 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 CA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 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.17: 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.20: 6 residues within 4Å: Chain F: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.25, F:F.146 CA.21: 6 residues within 4Å: Chain F: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.378, F:N.508, F:D.511, F:D.512 CA.24: 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.25: 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.28: 6 residues within 4Å: Chain H: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.25, H:F.146 CA.29: 6 residues within 4Å: Chain H: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.378, H:N.508, H:D.511, H:D.512 CA.30: 6 residues within 4Å: Chain I: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.25, I:F.146 CA.31: 6 residues within 4Å: Chain I: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.378, I:N.508, I:D.511, I:D.512 CA.32: 6 residues within 4Å: Chain J: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.25, J:F.146 CA.33: 6 residues within 4Å: Chain J: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.378, J:N.508, J:D.511, J:D.512 CA.36: 6 residues within 4Å: Chain K: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.25, K:F.146 CA.37: 6 residues within 4Å: Chain K: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.378, K:N.508, K:D.511, K:D.512 CA.40: 6 residues within 4Å: Chain L: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.25, L:F.146 CA.41: 6 residues within 4Å: Chain L: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.378, L:N.508, L:D.511, L:D.512 CA.44: 6 residues within 4Å: Chain M: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.25, M:F.146 CA.45: 6 residues within 4Å: Chain M: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.378, M:N.508, M:D.511, M:D.512 CA.48: 6 residues within 4Å: Chain N: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.25, N:F.146 CA.49: 6 residues within 4Å: Chain N: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.378, N:N.508, N:D.511, N:D.512 CA.50: 6 residues within 4Å: Chain O: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.25, O:F.146 CA.51: 6 residues within 4Å: Chain O: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:D.378, O:N.508, O:D.511, O:D.512 CA.54: 6 residues within 4Å: Chain P: D.25, N.142, N.144, F.146, A.147, D.150 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.25, P:F.146 CA.55: 6 residues within 4Å: Chain P: D.378, N.504, N.506, N.508, D.511, D.512 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.378, P:N.508, P:D.511, P:D.512 CA.58: 6 residues within 4Å: Chain Q: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:D.116, Q:D.237, Q:I.239, Q:D.243 CA.59: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.61: 6 residues within 4Å: Chain R: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:D.116, R:D.237, R:I.239, R:D.243 CA.62: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.66: 6 residues within 4Å: Chain S: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:D.116, S:D.237, S:I.239, S:D.243 CA.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.70: 6 residues within 4Å: Chain T: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:D.116, T:D.237, T:I.239, T:D.243 CA.71: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.74: 6 residues within 4Å: Chain U: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:D.116, U:D.237, U:I.239, U:D.243 CA.75: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.78: 6 residues within 4Å: Chain V: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:D.116, V:D.237, V:I.239, V:D.243 CA.79: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.80: 6 residues within 4Å: Chain W: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:D.116, W:D.237, W:I.239, W:D.243 CA.81: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.82: 6 residues within 4Å: Chain X: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:D.116, X:D.237, X:I.239, X:D.243 CA.83: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.86: 6 residues within 4Å: Chain Y: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:D.116, Y:D.237, Y:I.239, Y:D.243 CA.87: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.89: 6 residues within 4Å: Chain Z: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:D.116, Z:D.237, Z:I.239, Z:D.243 CA.90: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.93: 6 residues within 4Å: Chain 0: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:D.116, 0:D.237, 0:I.239, 0:D.243 CA.94: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.97: 6 residues within 4Å: Chain 1: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:D.116, 1:D.237, 1:I.239, 1:D.243 CA.98: 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: ACEFGHIJKLMNOP
von Willebrand factor: BDQRSTUVWXYZ01

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
E

F
G

G
I

H
K

I
M

J
O

K
Q

L
S

M
U

N
W

O
Y

P
a

B
Z

D
b

Q
C

R
D

S
F

T
H

U
J

V
L

W
N

X
P

Y
R

Z
T

0
V

1
X

von Willebrand antigen 2

von Willebrand factor

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