SMTL ID : 1fe8.4 (3 other biounits)

CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

hetero-6-6-6-mer

Ligands

6 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 6 residues within 4Å: Chain A: K.73, A.74 Chain B: N.56, T.57, T.58 Ligands: NAG.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.73 Water bridges: A:A.74 Hydrogen bonds: B:N.56, B:T.57, B:T.57 NAG-FUC.2: 3 residues within 4Å: Chain E: N.56, T.57 Ligands: NAG.6 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Water bridges: D:A.74 Hydrogen bonds: E:N.56, E:T.57, E:T.57 NAG-FUC.3: 3 residues within 4Å: Chain H: G.55, N.56, T.57 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Water bridges: G:A.74 Hydrogen bonds: H:N.56, H:T.57 NAG-FUC.7: 6 residues within 4Å: Chain J: K.73, A.74 Chain K: N.56, T.57, T.58 Ligands: NAG.10 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:K.73 Water bridges: J:A.74 Hydrogen bonds: K:N.56, K:T.57, K:T.57 NAG-FUC.8: 3 residues within 4Å: Chain N: N.56, T.57 Ligands: NAG.12 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain N Water bridges: M:A.74, M:E.72 Hydrogen bonds: N:N.56, N:T.57, N:T.57 NAG-FUC.9: 3 residues within 4Å: Chain Q: G.55, N.56, T.57 3 PLIP interactions: 1 interactions with chain P, 2 interactions with chain Q Water bridges: P:A.74 Hydrogen bonds: Q:N.56, Q:T.57

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.4: 2 residues within 4Å: Ligands: NAG-FUC.1, NAG-FUC.1 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Ligands: NAG-FUC.2, NAG-FUC.2 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Ligands: NAG-FUC.7, NAG-FUC.7 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Ligands: NAG-FUC.8, NAG-FUC.8 No protein-ligand interaction detected (PLIP)

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 5 residues within 4Å: Chain C: K.142, D.143, W.163 Chain L: T.7, S.22 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain L Hydrogen bonds: C:K.142, C:D.143, L:S.22 Water bridges: C:I.144 CAC.11: 5 residues within 4Å: Chain C: T.7, S.22 Chain L: K.142, D.143, W.163 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C Hydrogen bonds: L:K.142, C:S.22 Water bridges: L:I.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romijn, R.A. et al., Identification of the collagen-binding site of the von Willebrand factor A3-domain. J.Biol.Chem. (2001)

Release Date

2001-04-04

Peptides

VON WILLEBRAND FACTOR: ADGJMP
IMMUNOGLOBULIN IGG RU5: BEHKNQ
IMMUNOGLOBULIN IGG RU5: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

J
A

M
B

P
C

B
H

E
I

H
J

K
H

N
I

Q
J

C
L

F
M

I
N

L
L

O
M

R
N

VON WILLEBRAND FACTOR

IMMUNOGLOBULIN IGG RU5

IMMUNOGLOBULIN IGG RU5

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