SMTL ID : 6vfr.1

Crystal structure of human protocadherin 18 EC1-EC4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

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: 5 residues within 4Å: Chain A: E.220, L.239, D.240, L.241, N.242 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 2 residues within 4Å: Chain A: H.377, N.393 No protein-ligand interaction detected (PLIP)

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.3: 3 residues within 4Å: Chain A: K.4, N.76, E.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.99

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-FUC.4: 4 residues within 4Å: Chain B: E.220, L.239, D.240, N.242 No protein-ligand interaction detected (PLIP)

18 x CA: CALCIUM ION(Non-covalent)

CA.5: 10 residues within 4Å: Chain A: N.104, N.106, S.107, P.108, D.136, D.138, N.142, S.143, D.193, R.199 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.106, A:D.136, A:D.136, A:N.142, A:D.193 CA.6: 7 residues within 4Å: Chain A: E.9, E.68, D.102, I.103, D.105, D.138 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.68, A:I.103, A:D.105, A:D.138 CA.7: 7 residues within 4Å: Chain A: E.9, E.10, D.66, R.67, E.68, D.105 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:E.10, A:D.66, A:E.68, A:D.105 CA.8: 7 residues within 4Å: Chain A: E.121, R.179, E.180, D.211, S.212, D.214, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.121, A:D.211, A:S.212, A:D.214, A:D.247 CA.9: 5 residues within 4Å: Chain A: E.121, D.178, R.179, E.180, D.214 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.121, A:D.178, A:E.180, A:D.214, H2O.1 CA.10: 9 residues within 4Å: Chain A: N.213, N.215, S.216, D.245, D.247, N.251, G.252, D.301 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.215, A:D.245, A:D.245, A:N.251, A:D.301 CA.11: 9 residues within 4Å: Chain A: E.230, Y.287, E.288, D.319, V.320, D.322, N.323, D.361 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.230, A:E.288, A:E.288, A:D.319, A:D.361 CA.12: 6 residues within 4Å: Chain A: E.230, D.286, E.288, D.322, N.323 Ligands: CA.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.230, A:D.286, A:E.288, A:D.322 CA.13: 8 residues within 4Å: Chain A: N.321, N.323, P.325, D.359, D.361, N.365, G.366, D.412 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.323, A:D.359, A:D.361, A:N.365, A:D.412 CA.22: 7 residues within 4Å: Chain B: E.9, E.68, D.102, I.103, D.105, D.138 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.68, B:I.103, B:D.105, B:D.138 CA.23: 6 residues within 4Å: Chain B: E.9, E.10, D.66, E.68, D.105 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.9, B:E.10, B:D.66, B:E.68, B:D.105 CA.24: 9 residues within 4Å: Chain B: N.104, N.106, S.107, P.108, D.136, D.138, N.142, S.143, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.106, B:D.136, B:D.136, B:N.142, B:D.193 CA.25: 8 residues within 4Å: Chain B: N.213, N.215, S.216, D.245, D.247, N.251, G.252, D.301 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.215, B:D.245, B:D.247, B:N.251, B:D.301 CA.26: 6 residues within 4Å: Chain B: E.121, D.178, R.179, E.180, D.214, N.215 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.121, B:D.178, B:E.180, B:D.214 CA.27: 7 residues within 4Å: Chain B: E.121, E.180, D.211, S.212, D.214, N.215, D.247 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.121, B:D.211, B:S.212, B:D.214, B:D.247 CA.28: 7 residues within 4Å: Chain B: E.230, D.286, Y.287, E.288, D.322, N.323 Ligands: CA.29 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.230, B:D.286, B:E.288, H2O.2, H2O.2 CA.29: 9 residues within 4Å: Chain B: E.230, Y.287, E.288, D.319, V.320, D.322, N.323, D.361 Ligands: CA.28 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.288, B:E.288, B:D.319, B:D.322, B:D.361 CA.30: 9 residues within 4Å: Chain B: N.321, N.323, P.325, D.359, D.361, N.365, G.366, D.412, L.418 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.323, B:D.359, B:D.361, B:N.365, B:D.412

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

EDO.14: 6 residues within 4Å: Chain A: N.152, D.153, F.154, K.182, Y.185, L.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.153, A:D.153 EDO.15: 10 residues within 4Å: Chain A: R.112, I.115, P.116, I.117, I.129, P.130, L.131, D.132 Chain B: S.260, H.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.112, A:D.132, A:D.132 EDO.16: 5 residues within 4Å: Chain A: D.319, S.362, G.363, L.364, N.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.362, A:L.364, A:N.365 EDO.17: 7 residues within 4Å: Chain A: S.21, L.28, L.29, P.34, S.35, V.37, F.39 No protein-ligand interaction detected (PLIP) EDO.18: 11 residues within 4Å: Chain A: N.213, D.214, N.215, S.216, P.217, D.301, P.304, N.305, S.306, I.307 Ligands: CA.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.213, A:D.301, A:I.307 EDO.31: 9 residues within 4Å: Chain A: S.260, H.261 Chain B: R.112, I.115, I.117, I.129, P.130, L.131, D.132 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.112, B:D.132 EDO.32: 7 residues within 4Å: Chain B: N.152, D.153, F.154, K.182, Y.185, E.186, L.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.153, B:D.153 EDO.33: 8 residues within 4Å: Chain B: N.213, D.214, N.215, S.216, D.301, N.305, S.306, I.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.213, B:I.307, B:I.307

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

NA.19: 5 residues within 4Å: Chain A: D.240, L.241, N.242, R.276, G.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.242 NA.34: 6 residues within 4Å: Chain B: D.240, L.241, N.242, R.276, G.277, H.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.241

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

NAG.20: 1 residues within 4Å: Chain B: N.393 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain B: N.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins. Cell Rep (2020)

Release Date

2020-03-11

Peptides

Protocadherin-18: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protocadherin-18