SMTL ID : 5z8y.1 (3 other biounits)

Crystal structure of human LRRTM2 in complex with Neurexin 1beta

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 4 residues within 4Å: Chain B: S.104, G.105, N.107, Y.121 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.210 NAG.3: 3 residues within 4Å: Chain A: N.93, H.116, E.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.93, A:E.118 NAG.4: 1 residues within 4Å: Chain A: N.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: H.20, H.39 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.20, A:H.39

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain B: D.60, V.77, I.129, F.130, N.131 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:D.60, B:V.77, B:I.129, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamagata, A. et al., Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction. Nat Commun (2018)

Release Date

2018-10-10

Peptides

Leucine-rich repeat transmembrane neuronal protein 2: A
Neurexin-1-beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Leucine-rich repeat transmembrane neuronal protein 2

Neurexin-1-beta

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