SMTL ID : 2v1w.1

Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: H.4, A.42, A.43, R.83, D.89 Chain B: G.36, L.41 Chain C: R.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.43, A:R.83, C:R.17 EDO.4: 8 residues within 4Å: Chain C: H.4, A.42, A.43, R.83, D.89 Chain D: G.36, L.41 Chain G: R.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrogen bonds: C:A.43, C:R.83, G:R.17 EDO.7: 8 residues within 4Å: Chain A: R.17 Chain E: H.4, A.42, A.43, R.83, D.89 Chain F: G.36, L.41 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:A.43, E:R.83, A:R.17 EDO.10: 8 residues within 4Å: Chain E: R.17 Chain G: H.4, A.42, A.43, R.83, D.89 Chain H: G.36, L.41 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:R.17, G:A.43, G:R.83

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: E.87, S.88 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.87, H2O.3, H2O.6, H2O.6, H2O.6, H2O.6 MG.5: 2 residues within 4Å: Chain D: E.87, S.88 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.87, H2O.9, H2O.11, H2O.11, H2O.11, H2O.11 MG.8: 2 residues within 4Å: Chain F: E.87, S.88 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.87, H2O.14, H2O.17, H2O.17, H2O.17, H2O.17 MG.11: 2 residues within 4Å: Chain H: E.87, S.88 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.87, H2O.20, H2O.22, H2O.22, H2O.23, H2O.23

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 10 residues within 4Å: Chain B: G.21, R.22, A.26, P.27, L.28, L.49, I.50, Q.51, T.58, E.59 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.26, B:L.28, B:Q.51, B:T.58 Water bridges: B:T.58 1PE.6: 10 residues within 4Å: Chain D: G.21, R.22, A.26, P.27, L.28, L.49, I.50, Q.51, T.58, E.59 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.26, D:L.28, D:Q.51, D:T.58 Water bridges: D:T.58 1PE.9: 10 residues within 4Å: Chain F: G.21, R.22, A.26, P.27, L.28, L.49, I.50, Q.51, T.58, E.59 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:A.26, F:L.28, F:Q.51, F:T.58 Water bridges: F:T.58 1PE.12: 10 residues within 4Å: Chain H: G.21, R.22, A.26, P.27, L.28, L.49, I.50, Q.51, T.58, E.59 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:A.26, H:L.28, H:Q.51, H:T.58 Water bridges: H:T.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elkins, J.M. et al., Unusual Binding Interactions in Pdz Domain Crystal Structures Help Explain Binding Mechanisms. Protein Sci. (2010)

Release Date

2007-06-12

Peptides

PDZ AND LIM DOMAIN PROTEIN 4: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

PDZ AND LIM DOMAIN PROTEIN 4