SMTL ID : 7wqt.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-16-16-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: V.60, F.75, N.77 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.134, N.144 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain B: N.94 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain B: N.384, A.387, P.388 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain C: N.77, T.79 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain C: N.134, N.142, N.144, D.149 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain D: N.94 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain 0: L.372 Chain D: N.384, C.386, A.387, P.388 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain E: N.94 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain E: N.384, C.386, P.388, H.413 Chain G: Y.377 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain G: N.94 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain E: Y.377 Chain G: N.384, A.387, P.388, H.413 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain 2: Y.377 Chain H: N.384, P.388 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain I: F.75, N.77 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain I: N.134 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain K: F.75, N.77, T.79 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain K: F.133, N.134 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain M: F.75, N.77 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain M: N.134 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain O: V.60, F.75, V.76, N.77, T.79, R.86 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain O: F.133, N.134 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain R: F.75, N.77, T.79 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain R: N.134 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain S: F.75, N.77, T.79, R.86 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain S: F.133, N.134 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain T: N.134 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain T: F.75, V.76, N.77 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain U: F.75, N.77, T.79 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain U: N.134, D.149 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain V: N.77, T.79 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain V: F.133, N.134 Ligand excluded by PLIP NAG.73: 1 residues within 4Å: Chain Y: N.94 Ligand excluded by PLIP NAG.74: 1 residues within 4Å: Chain Y: N.384 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain Z: N.94 Ligand excluded by PLIP NAG.78: 4 residues within 4Å: Chain B: Y.377 Chain Z: N.384, A.387, P.388 Ligand excluded by PLIP NAG.82: 2 residues within 4Å: Chain 0: Q.89, N.94 Ligand excluded by PLIP NAG.83: 4 residues within 4Å: Chain 0: N.384, S.385, A.387, P.388 Ligand excluded by PLIP NAG.85: 1 residues within 4Å: Chain 1: N.94 Ligand excluded by PLIP NAG.88: 2 residues within 4Å: Chain 2: Q.89, N.94 Ligand excluded by PLIP NAG.89: 4 residues within 4Å: Chain 2: V.354, N.384, C.386, H.413 Ligand excluded by PLIP NAG.96: 2 residues within 4Å: Chain 5: Q.89, N.94 Ligand excluded by PLIP NAG.97: 3 residues within 4Å: Chain 5: N.384, P.388 Chain Y: Y.377 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, D.149, 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.378, A:N.508, A:D.511, A:D.511, A:D.512 CA.7: 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.10: 6 residues within 4Å: Chain C: D.25, N.142, N.144, F.146, D.149, 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 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.378, C:N.508, C:D.511, C:D.511, C:D.512 CA.14: 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.17: 6 residues within 4Å: Chain E: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.116, E:D.237, E:I.239, E:D.243 CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.19: 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.22: 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.24: 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.27: 5 residues within 4Å: Chain I: D.25, N.142, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.25, I:F.146 CA.28: 6 residues within 4Å: Chain I: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.378, I:N.508, I:D.511, I:D.511, I:D.512 CA.29: 6 residues within 4Å: Chain J: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.116, J:D.237, J:I.239, J:D.243 CA.32: 6 residues within 4Å: Chain K: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.25, K:F.146 CA.33: 6 residues within 4Å: Chain K: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.378, K:N.508, K:D.511, K:D.511, K:D.512 CA.34: 6 residues within 4Å: Chain L: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.116, L:D.237, L:I.239, L:D.243 CA.37: 5 residues within 4Å: Chain M: D.25, N.142, N.144, F.146, D.150 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.25, M:F.146 CA.38: 6 residues within 4Å: Chain M: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:D.378, M:N.508, M:D.511, M:D.511, M:D.512 CA.39: 6 residues within 4Å: Chain N: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.25, N:F.146 CA.40: 6 residues within 4Å: Chain N: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.378, N:N.508, N:D.511, N:D.511, N:D.512 CA.43: 6 residues within 4Å: Chain O: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:D.25, O:F.146 CA.44: 6 residues within 4Å: Chain O: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:D.378, O:N.508, O:D.511, O:D.511, O:D.512 CA.45: 6 residues within 4Å: Chain P: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.25, P:F.146 CA.46: 6 residues within 4Å: Chain P: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:D.378, P:N.508, P:D.511, P:D.511, P:D.512 CA.47: 6 residues within 4Å: Chain Q: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.25, Q:F.146 CA.48: 6 residues within 4Å: Chain Q: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:D.378, Q:N.508, Q:D.511, Q:D.511, Q:D.512 CA.51: 6 residues within 4Å: Chain R: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:D.25, R:F.146 CA.52: 6 residues within 4Å: Chain R: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:D.378, R:N.508, R:D.511, R:D.511, R:D.512 CA.55: 6 residues within 4Å: Chain S: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:D.25, S:F.146 CA.56: 6 residues within 4Å: Chain S: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:D.378, S:N.508, S:D.511, S:D.511, S:D.512 CA.58: 6 residues within 4Å: Chain T: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:D.25, T:F.146 CA.59: 6 residues within 4Å: Chain T: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:D.378, T:N.508, T:D.511, T:D.511, T:D.512 CA.63: 6 residues within 4Å: Chain U: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:D.25, U:F.146 CA.64: 6 residues within 4Å: Chain U: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:D.378, U:N.508, U:D.511, U:D.511, U:D.512 CA.67: 6 residues within 4Å: Chain V: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:D.25, V:F.146 CA.68: 6 residues within 4Å: Chain V: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:D.378, V:N.508, V:D.511, V:D.511, V:D.512 CA.69: 6 residues within 4Å: Chain W: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:D.25, W:F.146 CA.70: 6 residues within 4Å: Chain W: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:D.378, W:N.508, W:D.511, W:D.511, W:D.512 CA.71: 6 residues within 4Å: Chain X: D.25, N.142, N.144, F.146, D.149, D.150 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:D.25, X:F.146 CA.72: 6 residues within 4Å: Chain X: D.378, N.504, N.506, N.508, D.511, D.512 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:D.378, X:N.508, X:D.511, X:D.511, X:D.512 CA.75: 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.76: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.79: 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.80: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.81: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.84: 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.86: 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.87: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.90: 6 residues within 4Å: Chain 2: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:D.116, 2:D.237, 2:I.239, 2:D.243 CA.91: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.92: 6 residues within 4Å: Chain 3: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:D.116, 3:D.237, 3:I.239, 3:D.243 CA.93: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.94: 6 residues within 4Å: Chain 4: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:D.116, 4:D.237, 4:I.239, 4:D.243 CA.95: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.98: 6 residues within 4Å: Chain 5: D.116, N.235, D.237, I.239, N.242, D.243 4 PLIP interactions: 4 interactions with chain 5 Metal complexes: 5:D.116, 5:D.237, 5:I.239, 5:D.243

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: ACIKMNOPQRSTUVWX
von Willebrand factor: BDEFGHJLYZ012345

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

I
E

K
F

M
G

N
H

O
I

P
J

Q
K

R
L

S
M

T
N

U
O

V
P

W
Q

X
R

B
a

D
b

E
C

F
c

G
D

H
d

J
e

L
f

Y
S

Z
T

0
U

1
V

2
W

3
X

4
Y

5
Z

von Willebrand antigen 2

von Willebrand factor

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