SMTL ID : 5szr.1 (2 other biounits)

Protocadherin Gamma B2 extracellular cadherin domains 3-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 3 residues within 4Å: Chain A: E.180, N.182, I.200 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.200

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 4 residues within 4Å: Chain A: I.255, Q.296, S.306, N.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.306, A:N.308 Water bridges: A:N.308

9 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.16, D.71, E.73, D.105 Ligands: CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.16, A:D.71, A:E.73, H2O.2, H2O.4 CA.4: 7 residues within 4Å: Chain A: E.16, E.73, D.102, E.103, D.105, D.138 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.16, A:E.73, A:E.73, A:D.102, A:D.138 CA.5: 6 residues within 4Å: Chain A: N.104, C.106, D.136, D.138, N.142, D.189 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.106, A:D.136, A:D.138, A:N.142, A:D.189 CA.6: 5 residues within 4Å: Chain A: E.121, D.174, E.176, D.210 Ligands: CA.7 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.121, A:D.174, A:E.176, A:D.210, H2O.3, H2O.4 CA.7: 8 residues within 4Å: Chain A: E.121, E.176, D.207, V.208, D.210, N.211, D.243 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.121, A:D.207, A:V.208, A:D.210, A:D.243 CA.8: 6 residues within 4Å: Chain A: N.209, N.211, D.241, D.243, N.247, D.299 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.211, A:D.241, A:D.243, A:N.247, A:D.299 CA.9: 5 residues within 4Å: Chain A: E.226, D.284, E.286, D.320 Ligands: CA.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.226, A:D.284, A:D.320, H2O.1, H2O.4 CA.10: 8 residues within 4Å: Chain A: E.226, E.286, D.317, R.318, D.320, N.321, D.360 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.226, A:E.286, A:E.286, A:D.317, A:R.318 CA.11: 6 residues within 4Å: Chain A: N.319, N.321, D.358, D.360, N.364, D.411 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.321, A:D.358, A:D.360, A:N.364, A:D.411

7 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.12: 4 residues within 4Å: Chain A: S.23, V.24, L.25, Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26 MAN.13: 4 residues within 4Å: Chain A: S.233, A.235, Q.236, V.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.235 MAN.14: 3 residues within 4Å: Chain A: R.410, P.416, S.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.410 MAN.15: 4 residues within 4Å: Chain A: L.406, T.420, A.421 Ligands: MAN.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.333 MAN.16: 8 residues within 4Å: Chain A: D.333, G.334, S.335, R.404, L.406, T.422, H.424 Ligands: MAN.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.333, A:S.335, A:R.404 MAN.17: 1 residues within 4Å: Chain A: S.196 No protein-ligand interaction detected (PLIP) MAN.18: 4 residues within 4Å: Chain A: H.216, S.238, A.239, S.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.216 Water bridges: A:Y.252

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.19: 4 residues within 4Å: Chain A: Q.217, S.219, Y.220, L.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217, A:S.219, A:L.221 EDO.20: 3 residues within 4Å: Chain A: G.362, H.363, W.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.366 EDO.21: 3 residues within 4Å: Chain A: S.77, T.79, Q.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:T.79, A:T.79 EDO.22: 3 residues within 4Å: Chain A: V.47, D.48, E.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.48, A:E.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goodman, K.M. et al., gamma-Protocadherin structural diversity and functional implications. Elife (2016)

Release Date

2016-10-19

Peptides

Protein Pcdhgb2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein Pcdhgb2

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