SMTL ID : 5iry.1

Crystal structure of human Desmocollin-1 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

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.1: 8 residues within 4Å: Chain A: V.341, V.343, K.407, N.408, Q.410, N.412, T.428, V.430 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: Q.30, N.31, Y.32 No protein-ligand interaction detected (PLIP)

24 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: E.11, N.12, D.67, R.68, E.69, D.103 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:D.67, A:D.67, A:E.69, A:D.103 CA.4: 8 residues within 4Å: Chain A: N.102, N.104, P.106, D.134, D.136, H.142, D.192, L.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:H.142, A:D.192 CA.5: 6 residues within 4Å: Chain A: N.214, N.216, D.245, D.247, H.253, N.304 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.216, A:D.245, A:D.245, A:D.247, A:H.253 CA.6: 9 residues within 4Å: Chain A: E.231, Y.290, E.291, D.330, S.331, D.332, E.333, E.365 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.231, A:E.291, A:D.330, A:S.331 CA.7: 5 residues within 4Å: Chain A: D.348, D.400, R.401, E.402, D.438 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.348, A:D.400, A:E.402, A:E.402, A:D.438 CA.8: 7 residues within 4Å: Chain A: D.348, R.401, E.402, D.435, Y.436, D.438, D.465 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.402, A:D.435, A:Y.436, A:D.438, A:D.465 CA.9: 9 residues within 4Å: Chain A: N.437, H.439, A.440, P.441, D.463, D.465, N.469, G.470, D.516 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.463, A:D.463, A:D.465, A:N.469, A:D.516 CA.10: 5 residues within 4Å: Chain A: E.231, N.289, E.291, E.333 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.231, A:E.291, A:E.291, A:E.333, A:E.333 CA.11: 4 residues within 4Å: Chain A: D.332, E.333, P.364, E.365 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.332, A:D.332, A:E.333, A:E.365, A:E.365 CA.12: 7 residues within 4Å: Chain A: E.11, E.69, D.100, D.101, D.103, N.104, D.136 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.11, A:E.69, A:D.100, A:D.101, A:D.103, A:D.136 CA.13: 7 residues within 4Å: Chain A: E.119, N.120, D.177, R.178, E.179, D.215, K.310 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.119, A:D.177, A:D.215 CA.14: 7 residues within 4Å: Chain A: E.119, R.178, E.179, D.212, E.213, D.215, D.247 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.119, A:D.212, A:D.215, A:D.247 CA.20: 6 residues within 4Å: Chain B: E.11, N.12, D.67, R.68, E.69, D.103 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:D.67, B:D.67, B:E.69, B:D.103 CA.21: 8 residues within 4Å: Chain B: N.102, N.104, A.105, P.106, D.134, D.136, H.142, D.192 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.104, B:D.134, B:D.136, B:H.142, B:D.192 CA.22: 10 residues within 4Å: Chain B: N.214, N.216, P.217, P.218, D.245, D.247, H.253, S.254, N.304, F.308 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.216, B:D.245, B:D.245, B:D.247, B:H.253 CA.23: 8 residues within 4Å: Chain B: E.231, Y.290, E.291, D.330, S.331, E.333, E.365 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.231, B:E.291, B:D.330, B:S.331, B:E.333 CA.24: 7 residues within 4Å: Chain B: E.231, N.232, N.289, Y.290, E.291, E.333 Ligands: CA.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.231, B:E.291, B:E.333, B:E.333 CA.25: 7 residues within 4Å: Chain B: D.348, D.400, R.401, E.402, D.438, H.439 Ligands: CA.26 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.400, B:E.402, B:D.438 CA.26: 8 residues within 4Å: Chain B: D.348, R.401, E.402, D.435, Y.436, D.438, D.465 Ligands: CA.25 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.348, B:E.402, B:D.435, B:Y.436, B:D.438 CA.27: 8 residues within 4Å: Chain B: N.437, H.439, A.440, D.463, D.465, N.469, G.470, D.516 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.439, B:D.463, B:D.465, B:N.469, B:D.516 CA.28: 7 residues within 4Å: Chain B: E.11, E.69, D.100, D.101, N.102, D.103, D.136 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:D.100, B:D.101, B:D.103, B:D.136 CA.29: 7 residues within 4Å: Chain B: E.119, R.178, E.179, D.212, E.213, D.215, D.247 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.179, B:D.212, B:E.213, B:D.215, B:D.247 CA.30: 6 residues within 4Å: Chain B: E.119, N.120, D.177, R.178, E.179, D.215 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.119, B:D.177, B:D.177, B:E.179, B:D.215 CA.31: 5 residues within 4Å: Chain B: D.332, E.333, D.363, P.364, E.365 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.332, B:E.333, B:D.363, B:E.365, B:E.365

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

MAN.15: 5 residues within 4Å: Chain A: S.126, V.127, G.128, K.129, V.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.126 MAN.16: 4 residues within 4Å: Chain A: L.377, V.416, C.425, T.426 No protein-ligand interaction detected (PLIP) MAN.17: 5 residues within 4Å: Chain A: I.187, F.201, T.203, G.204 Ligands: MAN.18 No protein-ligand interaction detected (PLIP) MAN.18: 7 residues within 4Å: Chain A: R.111, V.112, Q.185, I.187, G.204, T.205 Ligands: MAN.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.185 MAN.32: 5 residues within 4Å: Chain B: S.126, V.127, G.128, K.129, V.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.126 MAN.33: 6 residues within 4Å: Chain B: R.111, V.112, I.187, G.204, T.205 Ligands: MAN.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.111, B:R.111 MAN.34: 6 residues within 4Å: Chain B: V.416, V.418, G.422, S.424, C.425, T.426 No protein-ligand interaction detected (PLIP) MAN.35: 5 residues within 4Å: Chain B: R.111, I.187, T.203, G.204 Ligands: MAN.33 No protein-ligand interaction detected (PLIP) MAN.36: 6 residues within 4Å: Chain B: P.340, V.341, S.414, T.426, G.427, T.428 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.426

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

EDO.19: 3 residues within 4Å: Chain A: Q.151, I.153, D.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Structural basis of adhesive binding by desmocollins and desmogleins. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-06-22

Peptides

Desmocollin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Desmocollin-1