SMTL ID : 3tbd.1

Crystal Structure of domain VI and LE1 of human Netrin-G2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: P.39, E.103, N.105, R.236, R.238 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.111, E.283, S.285, Q.287, P.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.283 Water bridges: A:Q.287

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: L.77, D.80, E.82, T.88, S.262 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.77, A:E.82, A:T.88, A:S.262, H2O.4

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

PO4.4: 4 residues within 4Å: Chain A: M.160, S.161, R.163, R.175 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.161, A:S.161 Water bridges: A:S.161, A:R.163 Salt bridges: A:R.163, A:R.175 PO4.5: 9 residues within 4Å: Chain A: G.127, R.128, A.186, G.187, S.188, K.189, K.190, E.191, K.192 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.128, A:G.187, A:K.189, A:K.190, A:E.191, A:K.192 Water bridges: A:G.127, A:G.187 Salt bridges: A:R.128

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

CL.6: 2 residues within 4Å: Chain A: K.304, R.307 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: G.296, P.297, D.298, C.299, G.300 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brasch, J. et al., Crystal structure of the ligand binding domain of netrin g2. J.Mol.Biol. (2011)

Release Date

2011-11-02

Peptides

Netrin-G2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Netrin-G2