SMTL ID : 7pmv.1

VWF Tubules of D1D2D'D3 domains

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: Q.77, V.82, F.97, N.99, G.100, T.101, T.103, R.108 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.101 NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: F.97, N.99, T.101, T.103, R.108 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.97 NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: V.82, F.97, N.99, T.101 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.97

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain D: F.97, N.99, T.101, R.108 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.108, D:R.108

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

NAG.5: 3 residues within 4Å: Chain A: F.155, N.156, N.166 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: N.1147, S.1148, A.1150, P.1151, H.1176 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: R.852, K.855, N.857 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: G.662, T.663, N.666, P.691 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: F.155, N.156, N.166 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain B: N.1147, S.1148, A.1150, P.1151, H.1176 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.857 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain B: T.663, N.666, L.667, L.693, Y.694 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: F.155, N.156, N.166, F.168 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: N.1147, S.1148, P.1151, H.1176 Chain D: R.1136 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.857 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain C: T.663, C.665, N.666, P.691, L.693, Y.694 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: F.155, N.156, N.166 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain D: N.1147, S.1148, A.1150, P.1151, H.1176 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.857 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain D: C.665, N.666, L.672, P.675, C.679 Ligand excluded by PLIP

12 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: D.47, N.164, N.166, F.168, A.169, D.172 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.47, A:N.166, A:F.168, A:D.172, A:D.172 CA.10: 7 residues within 4Å: Chain A: D.879, N.998, D.1000, G.1001, I.1002, N.1005, D.1006 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.879, A:D.1000, A:I.1002, A:D.1006, A:D.1006 CA.11: 7 residues within 4Å: Chain A: D.400, N.526, N.528, N.530, Q.531, 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.16: 8 residues within 4Å: Chain B: D.879, N.998, F.999, D.1000, G.1001, I.1002, N.1005, D.1006 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.879, B:D.1000, B:D.1000, B:D.1006, B:D.1006 CA.17: 7 residues within 4Å: Chain B: D.47, N.164, N.166, F.168, A.169, D.171, D.172 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.47, B:F.168, B:D.172, B:D.172 CA.18: 7 residues within 4Å: Chain B: D.400, N.526, N.528, N.530, Q.531, 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.23: 6 residues within 4Å: Chain C: N.164, N.166, F.168, A.169, D.171, D.172 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:F.168, C:D.171 CA.24: 8 residues within 4Å: Chain C: D.879, N.998, F.999, D.1000, G.1001, I.1002, N.1005, D.1006 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.879, C:D.1000, C:I.1002, C:D.1006, C:D.1006 CA.25: 7 residues within 4Å: Chain C: D.400, N.526, N.528, N.530, Q.531, 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.30: 8 residues within 4Å: Chain D: D.879, N.998, F.999, D.1000, G.1001, I.1002, N.1005, D.1006 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.879, D:D.1000, D:D.1000, D:D.1006, D:D.1006 CA.31: 6 residues within 4Å: Chain D: D.47, N.164, F.165, N.166, F.168, D.172 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.47, D:N.164, D:F.168, D:D.172, D:D.172 CA.32: 6 residues within 4Å: Chain D: D.400, N.526, N.528, N.530, Q.531, D.534 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.400, D:N.526, D:N.530, D:D.534, D:D.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Javitt, G. et al., Helical self-assembly of a mucin segment suggests an evolutionary origin for von Willebrand factor tubules. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-02-23

Peptides

von Willebrand factor: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

von Willebrand factor