SMTL ID : 6rk1.1

Crystal structure of TSP1 domain from CCN3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: N.8, C.9, I.10, Q.12, N.33, C.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.8, A:I.10, A:Q.12, A:N.33

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: T.44, R.45 Chain B: T.44, R.45 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.44, B:T.44, B:T.44, B:R.45, A:T.44, A:T.44, A:R.45 NA.3: 1 residues within 4Å: Chain A: E.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.11, A:E.11 NA.4: 1 residues within 4Å: Chain A: T.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.13 Water bridges: A:T.13

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: E.15, W.16 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: Q.43, R.45 Chain B: R.45, L.46 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: L.36, Q.37 Chain B: G.24, P.51, C.52 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: I.10, E.11 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.45, L.46 Chain B: Q.43, R.45 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: E.15, W.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, E.R. et al., The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers. Acta Crystallogr D Struct Biol (2020)

Release Date

2019-10-02

Peptides

CCN family member 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CCN family member 3