SMTL ID : 4pbp.1

crystal structure of zebrafish short-chain pentraxin protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.142, D.144, Q.154 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.142, A:D.144, H2O.4, H2O.4, H2O.4 CA.2: 4 residues within 4Å: Chain A: D.63, D.142, P.143, D.144 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.63, A:D.142, A:P.143, H2O.4, H2O.4 CA.5: 3 residues within 4Å: Chain B: D.142, D.144, Q.154 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.142, B:D.144, H2O.14, H2O.15, H2O.15 CA.6: 4 residues within 4Å: Chain B: D.63, D.142, P.143, D.144 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.63, B:D.142, B:P.143, H2O.14, H2O.15 CA.8: 3 residues within 4Å: Chain C: D.142, D.144, Q.154 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.142, C:D.144, H2O.24, H2O.24, H2O.24 CA.9: 4 residues within 4Å: Chain C: D.63, D.142, P.143, D.144 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.63, C:D.142, C:P.143, H2O.24, H2O.24

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: S.32, L.33, S.34, A.35, D.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.34, A:A.35, A:D.167 Water bridges: A:S.34, A:S.34 GOL.4: 6 residues within 4Å: Chain A: E.51, D.63, W.68, E.70, Y.78, S.82 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.63, A:E.70, A:S.82 Water bridges: A:E.51, A:N.66, A:E.70, A:Q.154, A:Q.154, A:Q.154, A:Q.154 GOL.7: 6 residues within 4Å: Chain B: E.51, D.63, W.68, E.70, Y.78, S.82 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.63, B:E.70, B:S.82, B:Q.154 Water bridges: B:N.66, B:E.70, B:Y.78, B:Y.78, B:S.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, R. et al., Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces. J.Struct.Biol. (2015)

Release Date

2015-03-25

Peptides

C-reactive protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

C-reactive protein