SMTL ID : 8a1f.1

Human PTPRK N-terminal domains MAM-Ig-FN1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

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 A: K.75, E.76, N.77, W.136 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 9 residues within 4Å: Chain A: T.98, N.100, N.112, P.113, N.116, W.205, G.211, E.212, D.213 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.205 Hydrogen bonds: A:N.112, A:D.213, A:D.213, A:D.213

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.3: 4 residues within 4Å: Chain B: K.75, E.76, N.77, W.136 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 9 residues within 4Å: Chain B: T.98, N.100, N.112, P.113, N.116, T.118, W.205, E.212, D.213 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.205 Hydrogen bonds: B:N.112, B:D.213, B:D.213

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

NAG.5: 3 residues within 4Å: Chain A: G.185, Q.186, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.186 NAG.7: 3 residues within 4Å: Chain B: Q.186, N.187, Q.234 No protein-ligand interaction detected (PLIP)

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

NA.6: 3 residues within 4Å: Chain A: T.13, S.52, D.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.13 NA.8: 3 residues within 4Å: Chain B: T.13, S.52, D.159 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hay, I.M. et al., Determinants of receptor tyrosine phosphatase homophilic adhesion: Structural comparison of PTPRK and PTPRM extracellular domains. J.Biol.Chem. (2023)

Release Date

2023-03-15

Peptides

Receptor-type tyrosine-protein phosphatase kappa: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Receptor-type tyrosine-protein phosphatase kappa