SMTL ID : 3be8.1

Crystal structure of the synaptic protein neuroligin 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71 Water bridges: A:R.25 NAG.2: 7 residues within 4Å: Chain A: Q.446, S.447, E.448, E.475, S.478, C.479, N.480 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.448, A:E.448, A:E.448, A:E.475 NAG.10: 1 residues within 4Å: Chain B: N.71 No protein-ligand interaction detected (PLIP) NAG.11: 6 residues within 4Å: Chain B: Q.446, S.447, E.448, S.478, C.479, N.480 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.448, B:N.480

2 x FLC: CITRATE ANION(Non-covalent)

FLC.3: 7 residues within 4Å: Chain A: Y.442, H.443, H.540, G.542, L.543, K.544, R.546 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.540, A:L.543, A:K.544 Salt bridges: A:H.443, A:H.540, A:H.540, A:K.544, A:K.544, A:R.546 FLC.13: 7 residues within 4Å: Chain B: Y.442, H.443, H.540, G.542, L.543, K.544, R.546 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:H.540, B:L.543, B:K.544 Water bridges: B:H.444, B:K.544, B:K.544 Salt bridges: B:H.443, B:H.540, B:H.540, B:K.544, B:K.544, B:R.546, B:R.546

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 9 residues within 4Å: Chain A: M.92, L.93, P.94, G.143, G.144, S.145, G.223, A.224, H.458 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.144, A:S.145, A:A.224 Salt bridges: A:H.458 PO4.14: 9 residues within 4Å: Chain B: M.92, L.93, P.94, G.143, G.144, S.145, G.223, A.224, H.458 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.144, B:S.145, B:A.224 Salt bridges: B:H.458

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

CL.5: 5 residues within 4Å: Chain A: A.48, S.49, P.50, P.63, S.64 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: R.552, A.553, T.554, K.555 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: W.96, Y.140, H.142, G.143, M.153 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain B: W.96, Y.140, H.142, G.143, M.153 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: A.48, S.49, P.50, P.63, S.64 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.552, A.553, T.554, K.555 Ligand excluded by PLIP

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

NA.7: 3 residues within 4Å: Chain A: L.31, N.33, L.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.31, A:L.31

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: S.181, G.183, D.184, Q.185, A.187, K.188, V.312, I.313, D.314 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.181, A:S.181, A:G.183, A:Q.185 Water bridges: A:I.313 GOL.17: 10 residues within 4Å: Chain B: S.181, G.183, D.184, Q.185, A.187, K.188, P.262, V.312, I.313, D.314 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.181, B:S.181, B:G.183, B:Q.185 Water bridges: B:I.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabrichny, I.P. et al., Structural Analysis of the Synaptic Protein Neuroligin and Its beta-Neurexin Complex: Determinants for Folding and Cell Adhesion. Neuron (2007)

Release Date

2008-01-29

Peptides

Neuroligin-4, X-linked: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neuroligin-4, X-linked

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