SMTL ID : 5erp.1

Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 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.1: 8 residues within 4Å: Chain A: I.240, T.304, I.305, K.306, N.307, I.309, N.311, G.329 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.2: 8 residues within 4Å: Chain B: T.304, I.305, K.306, N.307, I.309, Y.310, N.311 Ligands: EDO.42 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.309 NAG-NAG-BMA-MAN.3: 7 residues within 4Å: Chain B: E.358, V.360, I.393, N.394, D.395, T.396, A.397 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.358, B:V.360 Hydrogen bonds: B:E.358

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

MAN.4: 4 residues within 4Å: Chain A: K.87, T.103, S.104 Ligands: MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.87 MAN.5: 7 residues within 4Å: Chain A: E.11, T.12, Q.85, K.87, S.104, T.105 Ligands: MAN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.85, A:T.105 MAN.6: 6 residues within 4Å: Chain A: L.315, R.322, T.323, C.324, T.325 Ligands: MAN.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.323 MAN.7: 3 residues within 4Å: Chain A: L.276, T.325 Ligands: MAN.6 No protein-ligand interaction detected (PLIP) MAN.25: 7 residues within 4Å: Chain B: E.11, T.12, Q.85, K.87, S.104, T.105 Ligands: MAN.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.11, B:E.11, B:Q.85 MAN.26: 3 residues within 4Å: Chain B: K.87, T.103 Ligands: MAN.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.87 MAN.27: 5 residues within 4Å: Chain B: L.315, R.322, T.323, T.325 Ligands: MAN.28 No protein-ligand interaction detected (PLIP) MAN.28: 3 residues within 4Å: Chain B: T.325, G.326 Ligands: MAN.27 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: N.157, T.159, E.205 No protein-ligand interaction detected (PLIP) NAG.9: 6 residues within 4Å: Chain A: E.358, V.360, I.393, N.394, T.396, A.397 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.394 NAG.24: 3 residues within 4Å: Chain B: N.157, T.159, E.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.157

21 x CA: CALCIUM ION(Non-covalent)

CA.10: 7 residues within 4Å: Chain A: N.2, N.4, D.34, D.36, H.42, T.43, D.92 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.4, A:D.34, A:D.34, A:H.42, A:D.92 CA.11: 7 residues within 4Å: Chain A: E.19, N.20, D.77, R.78, E.79, D.115, H.116 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.19, A:D.77, A:D.115, H2O.1, H2O.2 CA.12: 8 residues within 4Å: Chain A: E.19, R.78, E.79, D.112, V.113, D.115, H.116, D.147 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.19, A:E.79, A:D.112, A:V.113, A:D.147 CA.13: 6 residues within 4Å: Chain A: E.131, N.132, N.189, E.191, E.232 Ligands: CA.14 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.131, A:E.191, A:E.232, A:E.232, H2O.2 CA.14: 8 residues within 4Å: Chain A: E.131, Y.190, E.191, D.229, Q.230, E.232, E.264 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.191, A:D.229, A:Q.230, A:E.232, A:E.264 CA.15: 9 residues within 4Å: Chain A: N.114, H.116, L.117, P.118, D.145, D.147, N.153, W.154, N.204 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.116, A:D.145, A:D.145, A:D.147, A:N.153 CA.16: 8 residues within 4Å: Chain A: E.247, R.300, E.301, D.334, V.335, D.337, N.338, D.365 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.247, A:E.301, A:V.335, A:D.337, A:D.365 CA.17: 4 residues within 4Å: Chain A: E.247, D.299, E.301, D.337 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.247, A:D.299, A:E.301, A:D.337, H2O.1 CA.18: 6 residues within 4Å: Chain A: D.231, E.232, D.262, P.263, E.264, R.322 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.231, A:E.232, A:D.262, A:E.264, H2O.1 CA.19: 7 residues within 4Å: Chain A: N.336, N.338, D.363, D.365, H.369, G.370, D.419 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.338, A:D.363, A:D.363, A:D.365, A:H.369 CA.29: 9 residues within 4Å: Chain B: N.2, N.4, P.6, D.34, D.36, H.42, T.43, D.92, L.100 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.4, B:D.34, B:D.34, B:H.42, B:D.92 CA.30: 8 residues within 4Å: Chain B: E.19, R.78, E.79, D.112, V.113, D.115, H.116, D.147 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:E.19, B:E.79, B:D.112, B:V.113, B:D.115, B:D.147 CA.31: 6 residues within 4Å: Chain B: E.19, N.20, D.77, E.79, D.115, H.116 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.19, B:E.79, B:D.115, H2O.3, H2O.4 CA.32: 8 residues within 4Å: Chain B: N.114, H.116, P.118, D.145, D.147, N.153, W.154, N.204 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.116, B:D.145, B:D.145, B:D.147, B:N.153 CA.33: 7 residues within 4Å: Chain B: E.131, N.132, N.189, Y.190, E.191, E.232 Ligands: CA.34 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.131, B:E.191, B:E.232, B:E.232, H2O.3 CA.34: 9 residues within 4Å: Chain B: E.131, Y.190, E.191, D.229, Q.230, E.232, P.263, E.264 Ligands: CA.33 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.191, B:D.229, B:Q.230, B:E.232, B:E.264 CA.35: 5 residues within 4Å: Chain B: D.231, E.232, D.262, E.264, R.322 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.231, B:E.232, B:D.262, B:E.264, H2O.4 CA.36: 6 residues within 4Å: Chain B: E.247, D.299, R.300, E.301, D.337, N.338 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.247, B:D.299, B:D.337, H2O.3, H2O.4 CA.37: 8 residues within 4Å: Chain B: E.247, R.300, E.301, D.334, V.335, D.337, N.338, D.365 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.247, B:E.301, B:D.334, B:V.335, B:D.365 CA.38: 9 residues within 4Å: Chain B: N.336, N.338, S.339, D.363, D.365, H.369, G.370, D.419, M.423 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.338, B:D.363, B:D.365, B:H.369, B:D.419 CA.39: 4 residues within 4Å: Chain A: E.179 Chain B: D.229, D.231, E.264 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.20: 2 residues within 4Å: Chain A: T.9, C.31 No protein-ligand interaction detected (PLIP) SO4.40: 3 residues within 4Å: Chain B: K.170, V.172, C.183 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.170

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

EDO.21: 7 residues within 4Å: Chain A: V.53, P.54, K.83, Y.84, Q.85, I.107 Chain B: T.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.85 EDO.22: 1 residues within 4Å: Chain A: D.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.3 EDO.23: 7 residues within 4Å: Chain A: N.168, P.187, L.188, N.189, E.192, K.193, M.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.168 EDO.41: 6 residues within 4Å: Chain B: I.160, L.161, K.162, G.163, N.164, E.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.163 EDO.42: 9 residues within 4Å: Chain B: I.240, Q.241, T.242, I.309, N.311, T.327, L.328, G.329 Ligands: NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.311, B:N.311

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

2016-06-15

Peptides

Desmocollin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Desmocollin-2