SMTL ID : 3r68.2 (1 other biounit)

Molecular Analysis of the PDZ3 domain of PDZK1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: D.35 Chain B: K.34, D.35 Ligands: ACT.15 No protein-ligand interaction detected (PLIP) ACT.2: 4 residues within 4Å: Chain A: H.4, R.7, K.48, D.86 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.5, A:K.48 Salt bridges: A:H.4, A:R.7, A:K.48 ACT.15: 4 residues within 4Å: Chain A: K.34, D.35 Chain B: D.35 Ligands: ACT.1 No protein-ligand interaction detected (PLIP) ACT.16: 4 residues within 4Å: Chain B: H.4, R.7, K.48, D.86 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.5, B:K.48 Salt bridges: B:H.4, B:R.7, B:K.48

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

EDO.3: 10 residues within 4Å: Chain A: N.16, G.17, Y.18, G.19, F.20, Y.21 Chain B: H.66 Ligands: CL.9, ZN.19, ZN.20 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.16, A:Y.18, A:G.19, A:F.20, A:F.20 EDO.17: 10 residues within 4Å: Chain A: H.66 Chain B: N.16, G.17, Y.18, G.19, F.20, Y.21 Ligands: ZN.5, ZN.6, CL.23 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.16, B:Y.18, B:G.19, B:F.20, B:F.20

8 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 1 residues within 4Å: Chain A: E.62 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.62 ZN.5: 6 residues within 4Å: Chain A: D.67 Chain B: K.13 Ligands: ZN.6, EDO.17, CL.22, CL.23 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.67, A:D.67, H2O.3 ZN.6: 3 residues within 4Å: Ligands: ZN.5, ZN.7, EDO.17 No protein-ligand interaction detected (PLIP) ZN.7: 5 residues within 4Å: Chain A: H.66 Ligands: ZN.6, CL.10, ZN.21, CL.24 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.66, H2O.1, H2O.3, H2O.7 ZN.18: 1 residues within 4Å: Chain B: E.62 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.62 ZN.19: 6 residues within 4Å: Chain A: K.13 Chain B: D.67 Ligands: EDO.3, CL.8, CL.9, ZN.20 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.67, B:D.67, H2O.7 ZN.20: 3 residues within 4Å: Ligands: EDO.3, ZN.19, ZN.21 No protein-ligand interaction detected (PLIP) ZN.21: 5 residues within 4Å: Chain B: H.66 Ligands: ZN.7, CL.10, ZN.20, CL.24 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.66, H2O.3, H2O.5, H2O.7

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

CL.8: 6 residues within 4Å: Chain A: K.13, Y.18, R.74 Chain B: D.67 Ligands: CL.9, ZN.19 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain A: K.13, G.17, Y.18 Chain B: D.67 Ligands: EDO.3, CL.8, ZN.19 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: Y.21, L.22, H.66 Chain B: H.66 Ligands: ZN.7, ZN.21, CL.24 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: E.71, K.75 Ligands: CL.13, CA.14 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: E.71 Ligands: CL.11, CA.14 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain A: D.67 Chain B: K.13, Y.18, R.74 Ligands: ZN.5, CL.23 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain A: D.67 Chain B: K.13, G.17, Y.18 Ligands: ZN.5, EDO.17, CL.22 Ligand excluded by PLIP CL.24: 7 residues within 4Å: Chain A: H.66 Chain B: Y.21, L.22, H.66 Ligands: ZN.7, CL.10, ZN.21 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: E.71, K.75 Ligands: CL.27, CA.28 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: E.71 Ligands: CL.25, CA.28 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.12: 3 residues within 4Å: Ligands: CA.14, CA.26, CA.28 No protein-ligand interaction detected (PLIP) CA.14: 5 residues within 4Å: Chain A: E.71 Ligands: CL.11, CA.12, CL.13, CA.26 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 CA.26: 3 residues within 4Å: Ligands: CA.12, CA.14, CA.28 No protein-ligand interaction detected (PLIP) CA.28: 5 residues within 4Å: Chain B: E.71 Ligands: CA.12, CL.25, CA.26, CL.27 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.71, B:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kocher, O. et al., Identification of the PDZ3 Domain of the Adaptor Protein PDZK1 as a Second, Physiologically Functional Binding Site for the C Terminus of the High Density Lipoprotein Receptor Scavenger Receptor Class B Type I. J.Biol.Chem. (2011)

Release Date

2011-05-18

Peptides

Na(+)/H(+) exchange regulatory cofactor NHE-RF3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Na(+)/H(+) exchange regulatory cofactor NHE-RF3

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