SMTL ID : 5afb.1

Crystal structure of the Latrophilin3 Lectin and Olfactomedin Domains

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.72, N.73, K.107 Chain D: I.223 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:I.223, D:I.223, A:N.72, A:N.73 NAG.6: 4 residues within 4Å: Chain B: N.72, N.73, K.107 Chain C: I.223 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:I.223, C:I.223, B:N.72, B:N.73 NAG.11: 4 residues within 4Å: Chain B: I.223 Chain C: N.72, N.73, K.107 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:I.223, B:I.223, C:N.72, C:N.73 NAG.16: 4 residues within 4Å: Chain A: I.223 Chain D: N.72, N.73, K.107 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:N.72, D:N.73, A:I.223, A:I.223

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

NA.2: 5 residues within 4Å: Chain A: G.190, F.191, D.244, L.245, D.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.190, A:L.245 NA.7: 5 residues within 4Å: Chain B: G.190, F.191, D.244, L.245, D.348 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.191, B:L.245 NA.12: 5 residues within 4Å: Chain C: G.190, F.191, D.244, L.245, D.348 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.244, C:L.245 NA.17: 5 residues within 4Å: Chain D: G.190, F.191, D.244, L.245, D.348 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.245, D:D.348

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.244, N.292, A.293, V.347 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.244, A:A.293, A:V.347, H2O.3, H2O.3 CA.8: 4 residues within 4Å: Chain B: D.244, N.292, A.293, V.347 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.244, B:A.293, B:V.347, H2O.7, H2O.7 CA.13: 4 residues within 4Å: Chain C: D.244, N.292, A.293, V.347 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.244, C:A.293, C:V.347, H2O.10, H2O.10 CA.18: 4 residues within 4Å: Chain D: D.244, N.292, A.293, V.347 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.244, D:A.293, D:V.347, H2O.13, H2O.13

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Q.144, K.148, Y.150, E.164, Y.180, L.213, R.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.144, A:Q.144, A:K.148, A:Y.150, A:E.164 GOL.5: 4 residues within 4Å: Chain A: T.28, Y.106, Q.144, A.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.145 Water bridges: A:L.143 GOL.9: 7 residues within 4Å: Chain B: Q.144, K.148, Y.150, E.164, Y.180, L.213, R.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.144, B:Q.144, B:K.148, B:E.164, B:Y.180 GOL.10: 4 residues within 4Å: Chain B: T.28, Y.106, Q.144, A.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.145 Water bridges: B:L.143 GOL.14: 7 residues within 4Å: Chain C: Q.144, K.148, Y.150, E.164, Y.180, L.213, R.214 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.144, C:Q.144, C:K.148, C:E.164, C:Y.180 GOL.15: 4 residues within 4Å: Chain C: T.28, Y.106, Q.144, A.145 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.145 Water bridges: C:L.143 GOL.19: 7 residues within 4Å: Chain D: Q.144, K.148, Y.150, E.164, Y.180, L.213, R.214 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.144, D:Q.144, D:K.148, D:Y.150, D:E.164 GOL.20: 4 residues within 4Å: Chain D: T.28, Y.106, Q.144, A.145 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.145 Water bridges: D:L.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jackson, V.A. et al., Structural Basis of Latrophilin-Flrt Interaction. Structure (2015)

Release Date

2015-03-18

Peptides

LATROPHILIN-3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

LATROPHILIN-3