SMTL ID : 8d3d.1

VWF tubule derived from dimeric D1-A1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

48 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.997, A:D.999, A:D.999, A:I.1001, A:D.1005 CA.2: 6 residues within 4Å: Chain A: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.400, A:N.530, A:D.533, A:D.534 CA.3: 6 residues within 4Å: Chain A: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.47, A:N.166, A:F.168, A:D.171, A:D.172 CA.9: 6 residues within 4Å: Chain B: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.997, B:D.999, B:D.999, B:I.1001, B:D.1005 CA.10: 6 residues within 4Å: Chain B: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.400, B:N.530, B:D.533, B:D.534 CA.11: 6 residues within 4Å: Chain B: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.47, B:N.166, B:F.168, B:D.171, B:D.172 CA.17: 6 residues within 4Å: Chain C: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.997, C:D.999, C:D.999, C:I.1001, C:D.1005 CA.18: 6 residues within 4Å: Chain C: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.400, C:N.530, C:D.533, C:D.534 CA.19: 6 residues within 4Å: Chain C: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.47, C:N.166, C:F.168, C:D.171, C:D.172 CA.25: 6 residues within 4Å: Chain D: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:N.997, D:D.999, D:D.999, D:I.1001, D:D.1005 CA.26: 6 residues within 4Å: Chain D: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.400, D:N.530, D:D.533, D:D.534 CA.27: 6 residues within 4Å: Chain D: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.47, D:N.166, D:F.168, D:D.171, D:D.172 CA.33: 6 residues within 4Å: Chain E: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:N.997, E:D.999, E:D.999, E:I.1001, E:D.1005 CA.34: 6 residues within 4Å: Chain E: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.400, E:N.530, E:D.533, E:D.534 CA.35: 6 residues within 4Å: Chain E: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.47, E:N.166, E:F.168, E:D.171, E:D.172 CA.41: 6 residues within 4Å: Chain F: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:N.997, F:D.999, F:D.999, F:I.1001, F:D.1005 CA.42: 6 residues within 4Å: Chain F: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.400, F:N.530, F:D.533, F:D.534 CA.43: 6 residues within 4Å: Chain F: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.47, F:N.166, F:F.168, F:D.171, F:D.172 CA.49: 6 residues within 4Å: Chain G: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:N.997, G:D.999, G:D.999, G:I.1001, G:D.1005 CA.50: 6 residues within 4Å: Chain G: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.400, G:N.530, G:D.533, G:D.534 CA.51: 6 residues within 4Å: Chain G: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.47, G:N.166, G:F.168, G:D.171, G:D.172 CA.57: 6 residues within 4Å: Chain H: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:N.997, H:D.999, H:D.999, H:I.1001, H:D.1005 CA.58: 6 residues within 4Å: Chain H: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.400, H:N.530, H:D.533, H:D.534 CA.59: 6 residues within 4Å: Chain H: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.47, H:N.166, H:F.168, H:D.171, H:D.172 CA.65: 6 residues within 4Å: Chain I: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:N.997, I:D.999, I:D.999, I:I.1001, I:D.1005 CA.66: 6 residues within 4Å: Chain I: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.400, I:N.530, I:D.533, I:D.534 CA.67: 6 residues within 4Å: Chain I: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.47, I:N.166, I:F.168, I:D.171, I:D.172 CA.73: 6 residues within 4Å: Chain J: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:N.997, J:D.999, J:D.999, J:I.1001, J:D.1005 CA.74: 6 residues within 4Å: Chain J: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.400, J:N.530, J:D.533, J:D.534 CA.75: 6 residues within 4Å: Chain J: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.47, J:N.166, J:F.168, J:D.171, J:D.172 CA.81: 6 residues within 4Å: Chain K: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:N.997, K:D.999, K:D.999, K:I.1001, K:D.1005 CA.82: 6 residues within 4Å: Chain K: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.400, K:N.530, K:D.533, K:D.534 CA.83: 6 residues within 4Å: Chain K: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:D.47, K:N.166, K:F.168, K:D.171, K:D.172 CA.89: 6 residues within 4Å: Chain L: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:N.997, L:D.999, L:D.999, L:I.1001, L:D.1005 CA.90: 6 residues within 4Å: Chain L: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.400, L:N.530, L:D.533, L:D.534 CA.91: 6 residues within 4Å: Chain L: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.47, L:N.166, L:F.168, L:D.171, L:D.172 CA.97: 6 residues within 4Å: Chain M: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:N.997, M:D.999, M:D.999, M:I.1001, M:D.1005 CA.98: 6 residues within 4Å: Chain M: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:D.400, M:N.530, M:D.533, M:D.534 CA.99: 6 residues within 4Å: Chain M: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:D.47, M:N.166, M:F.168, M:D.171, M:D.172 CA.105: 6 residues within 4Å: Chain N: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:N.997, N:D.999, N:D.999, N:I.1001, N:D.1005 CA.106: 6 residues within 4Å: Chain N: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:D.400, N:N.530, N:D.533, N:D.534 CA.107: 6 residues within 4Å: Chain N: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:D.47, N:N.166, N:F.168, N:D.171, N:D.172 CA.113: 6 residues within 4Å: Chain O: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:N.997, O:D.999, O:D.999, O:I.1001, O:D.1005 CA.114: 6 residues within 4Å: Chain O: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:D.400, O:N.530, O:D.533, O:D.534 CA.115: 6 residues within 4Å: Chain O: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:D.47, O:N.166, O:F.168, O:D.171, O:D.172 CA.121: 6 residues within 4Å: Chain P: D.878, N.997, D.999, I.1001, N.1004, D.1005 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:N.997, P:D.999, P:D.999, P:I.1001, P:D.1005 CA.122: 6 residues within 4Å: Chain P: D.400, N.526, N.528, N.530, D.533, D.534 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.400, P:N.530, P:D.533, P:D.534 CA.123: 6 residues within 4Å: Chain P: D.47, N.164, N.166, F.168, D.171, D.172 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:D.47, P:N.166, P:F.168, P:D.171, P:D.172

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

NAG.4: 4 residues within 4Å: Chain A: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.156 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: R.851, N.856 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.1146, P.1150 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.156 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: R.851, N.856 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.156 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: R.851, N.856 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.1146, P.1150 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.156 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: R.851, N.856 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain E: N.156 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: R.851, N.856 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.1146, P.1150 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain F: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain F: N.156 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain F: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain F: R.851, N.856 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain F: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain G: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain G: N.156 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain G: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain G: R.851, N.856 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain G: N.1146, P.1150 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain H: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain H: N.156 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain H: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain H: R.851, N.856 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain H: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.68: 4 residues within 4Å: Chain I: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.69: 1 residues within 4Å: Chain I: N.156 Ligand excluded by PLIP NAG.70: 4 residues within 4Å: Chain I: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.71: 2 residues within 4Å: Chain I: R.851, N.856 Ligand excluded by PLIP NAG.72: 2 residues within 4Å: Chain I: N.1146, P.1150 Ligand excluded by PLIP NAG.76: 4 residues within 4Å: Chain J: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.77: 1 residues within 4Å: Chain J: N.156 Ligand excluded by PLIP NAG.78: 4 residues within 4Å: Chain J: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.79: 2 residues within 4Å: Chain J: R.851, N.856 Ligand excluded by PLIP NAG.80: 3 residues within 4Å: Chain J: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.84: 4 residues within 4Å: Chain K: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.85: 1 residues within 4Å: Chain K: N.156 Ligand excluded by PLIP NAG.86: 4 residues within 4Å: Chain K: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.87: 2 residues within 4Å: Chain K: R.851, N.856 Ligand excluded by PLIP NAG.88: 2 residues within 4Å: Chain K: N.1146, P.1150 Ligand excluded by PLIP NAG.92: 4 residues within 4Å: Chain L: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.93: 1 residues within 4Å: Chain L: N.156 Ligand excluded by PLIP NAG.94: 4 residues within 4Å: Chain L: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.95: 2 residues within 4Å: Chain L: R.851, N.856 Ligand excluded by PLIP NAG.96: 3 residues within 4Å: Chain L: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.100: 4 residues within 4Å: Chain M: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.101: 1 residues within 4Å: Chain M: N.156 Ligand excluded by PLIP NAG.102: 4 residues within 4Å: Chain M: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.103: 2 residues within 4Å: Chain M: R.851, N.856 Ligand excluded by PLIP NAG.104: 2 residues within 4Å: Chain M: N.1146, P.1150 Ligand excluded by PLIP NAG.108: 4 residues within 4Å: Chain N: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.109: 1 residues within 4Å: Chain N: N.156 Ligand excluded by PLIP NAG.110: 4 residues within 4Å: Chain N: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.111: 2 residues within 4Å: Chain N: R.851, N.856 Ligand excluded by PLIP NAG.112: 3 residues within 4Å: Chain N: R.1144, N.1146, P.1150 Ligand excluded by PLIP NAG.116: 4 residues within 4Å: Chain O: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.117: 1 residues within 4Å: Chain O: N.156 Ligand excluded by PLIP NAG.118: 4 residues within 4Å: Chain O: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.119: 2 residues within 4Å: Chain O: R.851, N.856 Ligand excluded by PLIP NAG.120: 2 residues within 4Å: Chain O: N.1146, P.1150 Ligand excluded by PLIP NAG.124: 4 residues within 4Å: Chain P: F.97, N.99, T.101, R.108 Ligand excluded by PLIP NAG.125: 1 residues within 4Å: Chain P: N.156 Ligand excluded by PLIP NAG.126: 4 residues within 4Å: Chain P: N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.127: 2 residues within 4Å: Chain P: R.851, N.856 Ligand excluded by PLIP NAG.128: 3 residues within 4Å: Chain P: R.1144, N.1146, P.1150 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, J.R. et al., Structures of VWF tubules before and after concatemerization reveal a mechanism of disulfide bond exchange. Blood (2022)

Release Date

2022-07-06

Peptides

von Willebrand factor: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

von Willebrand factor

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