SMTL ID : 7n86.1 (1 other biounit)

Crystal Structure of Human Protocadherin-24 EC1-2 Form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

homo-dimer

Ligands

2 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.1: 8 residues within 4Å: Chain A: N.9, M.10, V.13, Q.24, F.26, W.27, V.29, M.90 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 8 residues within 4Å: Chain B: N.9, M.10, V.13, Q.24, F.26, W.27, V.29, M.90 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain A: T.150, D.152, S.153, N.175, K.176, Y.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.150, A:T.150, A:S.153, A:Y.180

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: N.1, V.2, D.32, D.34, D.36, D.81 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:V.2, A:D.32, A:D.32, A:D.36, A:D.81 CA.5: 7 residues within 4Å: Chain A: E.17, E.68, D.96, R.97, D.99, D.132 Ligands: NA.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.17, A:E.68, A:D.96, A:R.97, A:D.132 CA.6: 6 residues within 4Å: Chain A: N.98, N.100, D.130, D.132, A.136, D.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.100, A:D.130, A:A.136, A:D.188 CA.9: 6 residues within 4Å: Chain B: N.1, V.2, D.32, D.34, D.36, D.81 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.2, B:D.32, B:D.32, B:D.36 CA.10: 7 residues within 4Å: Chain B: E.17, E.68, D.96, R.97, D.99, N.100, D.132 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.68, B:D.96, B:R.97, B:D.99, B:D.132 CA.11: 7 residues within 4Å: Chain B: N.98, N.100, D.130, D.132, A.136, D.188, Q.200 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.100, B:D.130, B:D.132, B:A.136, B:D.188

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

CL.7: 2 residues within 4Å: Chain A: F.104, L.203 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: Q.105, V.129 Chain B: P.45, T.76 Ligand excluded by PLIP

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

NA.8: 6 residues within 4Å: Chain A: E.17, D.66, E.68, D.99, N.100 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.67, A:E.68, A:N.100 NA.14: 4 residues within 4Å: Chain B: E.17, D.66, E.68, D.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.17

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

IOD.12: 2 residues within 4Å: Chain A: P.45 Chain B: K.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gray, M.E. et al., Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent. Plos Biol. (2021)

Release Date

2021-09-01

Peptides

Cadherin-related family member 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-related family member 2

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