SMTL ID : 5nir.2 (1 other biounit)

Crystal structure of collagen 2A vWC domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.1: 11 residues within 4Å: Chain A: C.28, I.43, I.44, C.45, E.46, D.47, V.48, K.49, C.61, P.63 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.45, A:D.47

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: Q.12, R.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:R.29

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 2 residues within 4Å: Chain A: R.29 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.4: 8 residues within 4Å: Chain A: V.48, K.49, D.50, C.51, P.54, P.63, C.65 Ligands: P33.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.48, A:D.50, A:C.51 PEG.5: 5 residues within 4Å: Chain A: K.24, I.43, E.60, C.61, C.62 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.61, A:C.62 Water bridges: A:E.60, A:E.60 PEG.6: 4 residues within 4Å: Chain A: R.29, D.42 Ligands: PEG.3, PEG.7 No protein-ligand interaction detected (PLIP) PEG.7: 7 residues within 4Å: Chain A: Q.12, D.13, Q.15, P.25, E.26, R.29 Ligands: PEG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.13, A:E.26, A:R.29

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 8 residues within 4Å: Chain A: K.24, E.26, P.27, I.56, P.57, F.58, G.59, E.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.24, A:K.24, A:G.59 Water bridges: A:I.56 PG4.9: 3 residues within 4Å: Chain A: V.11, D.13, G.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.13, A:G.14 PG4.10: 5 residues within 4Å: Chain A: C.10, V.11, G.36, T.37, V.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.11, A:V.11, A:V.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, E.R. et al., Structural analyses of von Willebrand factor C domains of collagen 2A and CCN3 reveal an alternative mode of binding to bone morphogenetic protein-2. J. Biol. Chem. (2017)

Release Date

2017-06-14

Peptides

Collagen alpha-1(II) chain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Collagen alpha-1(II) chain

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