SMTL ID : 5ik5.1

Laminin A2LG45 C-form, G6/7 bound.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x A2G- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G-GAL.1: 4 residues within 4Å: Chain A: T.16, M.17, V.18, A.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.18 Water bridges: A:T.16, A:T.16

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: I.163, N.164 No protein-ligand interaction detected (PLIP)

1 x BDP- XYS- BDP- XYS: alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid

BDP-XYS-BDP-XYS.3: 12 residues within 4Å: Chain A: K.55, R.78, A.82, D.83, L.100, G.101, A.147, D.148, I.149, D.151 Ligands: CA.4, 4MU.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.148, A:I.149, A:K.55 Water bridges: A:D.151, A:D.151, A:D.151, A:D.151

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 7 residues within 4Å: Chain A: D.83, L.100, G.101, I.149, D.151 Ligands: BDP-XYS-BDP-XYS.3, BDP-XYS-BDP-XYS.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.83, A:L.100, A:I.149, A:D.151, H2O.2, H2O.14 CA.5: 6 residues within 4Å: Chain A: D.257, N.274, G.275, S.328, A.329, D.330 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.257, A:N.274, A:S.328, A:D.330, H2O.14

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.90, S.97, S.106, R.169, I.170, G.171, P.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.90, A:R.90 GOL.7: 3 residues within 4Å: Chain A: D.273, G.277, R.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.278 Water bridges: A:A.276, A:R.278, A:R.278 GOL.8: 5 residues within 4Å: Chain A: R.57, V.124, V.126, E.129, I.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.129 Water bridges: A:R.57 GOL.9: 9 residues within 4Å: Chain A: R.41, N.42, L.161, I.163, N.164, Y.165, P.172, T.174, Y.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.41, A:R.41, A:N.42, A:T.174 Water bridges: A:Y.165 GOL.10: 2 residues within 4Å: Chain A: T.166, R.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.168, A:R.168 GOL.11: 7 residues within 4Å: Chain A: I.282, Y.283, D.284, E.286, N.315, Q.316, V.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.284, A:D.284 Water bridges: A:E.286

1 x 4MU: 7-hydroxy-4-methyl-2H-chromen-2-one(Non-covalent)

4MU.12: 5 residues within 4Å: Chain A: G.101, S.102, G.103, K.145 Ligands: BDP-XYS-BDP-XYS.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.145 Water bridges: A:G.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Briggs, D.C. et al., Structural basis of laminin binding to the LARGE glycans on dystroglycan. Nat.Chem.Biol. (2016)

Release Date

2016-08-10

Peptides

Laminin subunit alpha-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laminin subunit alpha-2

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