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

Crystal structure of collagen 2A vWC domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: C.65, T.67 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.2: 7 residues within 4Å: Chain A: Q.12, D.13, Q.15, Y.17, W.23, P.25 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.17 EDO.3: 5 residues within 4Å: Chain A: P.25, E.26, R.29 Ligands: EDO.2, EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.26, A:R.29 EDO.4: 2 residues within 4Å: Chain A: R.29 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.26, A:R.29, A:R.29 EDO.5: 3 residues within 4Å: Chain A: E.6, R.16, N.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.16 EDO.6: 5 residues within 4Å: Chain A: C.45, D.47, I.56, C.61, P.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.47, A:C.61 EDO.7: 3 residues within 4Å: Chain A: T.67, L.69 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.67

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

PEG.8: 3 residues within 4Å: Chain A: P.25, E.26 Ligands: PG4.11 No protein-ligand interaction detected (PLIP) PEG.9: 3 residues within 4Å: Chain A: D.68, L.69, A.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.69

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

PG4.10: 6 residues within 4Å: Chain A: K.24, P.27, I.43, E.60, C.61, C.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.61, A:C.62 PG4.11: 10 residues within 4Å: Chain A: K.24, P.25, E.26, P.27, I.56, P.57, F.58, G.59, E.60 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.24, A:I.56, A:G.59 PG4.12: 6 residues within 4Å: Chain A: R.29, V.38, L.39, C.40, D.41, D.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.40, A:D.42

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
A

Collagen alpha-1(II) chain

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