SMTL ID : 7zwh.1

VWF Tubules of D1D2 and D'D3A1 domains

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 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: 6 residues within 4Å: Chain A: V.82, F.97, N.99, T.101, T.103, R.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain B: V.82, F.97, N.99, T.101, T.103, R.108 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.156, N.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.156 NAG.4: 6 residues within 4Å: Chain A: N.1147, S.1148, A.1150, P.1151, H.1174 Chain B: R.1136 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: R.852, N.857 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.852, A:N.857 NAG.6: 6 residues within 4Å: Chain A: T.663, N.666, P.691, G.692, L.693, Y.694 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.694 Hydrogen bonds: A:G.692, A:Y.694 NAG.10: 3 residues within 4Å: Chain B: N.156, N.166, F.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.156 NAG.11: 9 residues within 4Å: Chain B: R.1145, Y.1146, N.1147, S.1148, C.1149, A.1150, P.1151, H.1174, H.1176 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain B: N.857 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.857 NAG.13: 5 residues within 4Å: Chain B: T.663, N.666, P.691, G.692, Y.694 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.879, N.998, D.1000, I.1002, N.1005, D.1006 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.879, A:D.1000, A:D.1000, A:I.1002, A:D.1006 CA.8: 6 residues within 4Å: Chain A: D.47, N.164, N.166, F.168, D.171, D.172 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.47, A:N.164, A:D.172, A:D.172 CA.9: 6 residues within 4Å: Chain A: D.400, N.526, N.528, N.530, D.533, D.534 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.400, A:N.526, A:N.530, A:D.533, A:D.534 CA.14: 6 residues within 4Å: Chain B: D.879, N.998, D.1000, 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:I.1002, B:D.1006 CA.15: 6 residues within 4Å: Chain B: D.47, N.164, N.166, F.168, D.171, D.172 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.47, B:F.168, B:D.171, B:D.172 CA.16: 7 residues within 4Å: Chain B: S.398, F.399, D.400, C.524, G.525, N.526, Y.527 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.524, B:N.526

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Javitt, G. et al., Assembly of von Willebrand factor tubules with in vivo helical parameters requires A1 domain insertion. Blood (2022)

Release Date

2022-07-13

Peptides

von Willebrand factor: AB
von Willebrand factor: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
G

D
H

von Willebrand factor

von Willebrand factor