SMTL ID : 2yd9.1

Crystal structure of the N-terminal Ig1-3 module of Human Receptor Protein Tyrosine Phosphatase Sigma

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: I.140, Q.160 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: R.207, F.208 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: P.13, K.14, V.27 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: I.111, S.193 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: I.140, Q.160 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.207, F.208 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: P.13, K.14, V.27 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: I.111, S.193 Ligand excluded by PLIP

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 3 residues within 4Å: Chain A: L.129, S.163, A.165 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: V.204, G.231 Ligand excluded by PLIP IOD.7: 7 residues within 4Å: Chain A: Q.202, S.232, P.233, M.234 Chain B: Q.202, M.234 Ligands: IOD.18 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: P.115, Q.116, K.118, L.129 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain B: L.129, S.163, A.165 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain B: V.204, G.231 Ligand excluded by PLIP IOD.18: 7 residues within 4Å: Chain A: Q.202, M.234 Chain B: Q.202, S.232, P.233, M.234 Ligands: IOD.7 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain B: P.115, Q.116, K.118, L.129 Ligand excluded by PLIP

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

NAG.9: 3 residues within 4Å: Chain A: S.267, A.268, N.269 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.269 NAG.10: 4 residues within 4Å: Chain A: N.222, V.223, N.224, E.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.224, A:E.260 NAG.20: 3 residues within 4Å: Chain B: S.267, A.268, N.269 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.269 NAG.21: 4 residues within 4Å: Chain B: N.222, V.223, N.224, E.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.224

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.11: 9 residues within 4Å: Chain A: C.130, A.131, A.132, D.137, P.138, I.140, R.162, S.163, G.164 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.130, A:A.132, A:D.137, A:P.138, A:R.162 B3P.22: 9 residues within 4Å: Chain B: C.130, A.131, A.132, D.137, P.138, I.140, R.162, S.163, G.164 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.130, B:A.132, B:D.137, B:P.138, B:R.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coles, C.H. et al., Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension. Science (2011)

Release Date

2011-04-13

Peptides

RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S