SMTL ID : 6o3o.1

Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 (necl-5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-FUC.1: 4 residues within 4Å: Chain B: H.44, G.94, N.95, W.113 No protein-ligand interaction detected (PLIP)

2 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.2: 9 residues within 4Å: Chain B: R.140, N.163, S.165, L.180, I.182 Chain C: H.44, G.45, E.46 Ligands: NAG-NAG-BMA-FUC.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.180 Hydrogen bonds: B:R.140, B:R.140, C:G.45 Water bridges: B:S.165, B:T.178 NAG-NAG-BMA-FUC.9: 5 residues within 4Å: Chain C: E.93, G.94, N.95, W.113 Ligands: NAG-NAG-BMA-FUC.2 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.113

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 2 residues within 4Å: Chain B: T.210, N.212 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: V.22, N.74, T.76, F.78 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.22 Hydrogen bonds: A:N.74 NAG.5: 2 residues within 4Å: Chain A: N.131 Chain C: G.133 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.131, C:G.133 NAG.6: 4 residues within 4Å: Chain B: Y.25, V.70, N.80, S.82 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.70 Hydrogen bonds: B:S.82 NAG.7: 4 residues within 4Å: Chain B: N.288, T.290, A.295, Q.297 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain C: K.192, N.193, T.210 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.210 Hydrogen bonds: C:K.192, C:K.192 NAG.11: 5 residues within 4Å: Chain C: Y.25, V.70, A.71, N.80, S.82 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.25 Hydrogen bonds: C:N.80, C:S.82 NAG.12: 2 residues within 4Å: Chain C: N.288, Q.297 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.297 Hydrogen bonds: C:N.288 NAG.13: 5 residues within 4Å: Chain C: N.163, T.164, S.165, L.180, I.182 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain D: N.131, V.180, P.194 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.180 NAG.15: 9 residues within 4Å: Chain D: L.6, H.8, T.101, W.102, Q.103, N.170, F.171, T.172, K.174 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.6, D:F.171 Hydrogen bonds: D:H.8, D:Q.103, D:T.172, D:K.174, D:K.174 NAG.16: 5 residues within 4Å: Chain D: E.20, V.22, N.74, T.76, F.78 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.22 Hydrogen bonds: D:E.20, D:N.74, D:T.76 NAG.17: 1 residues within 4Å: Chain D: N.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.16

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

SO4.8: 5 residues within 4Å: Chain B: T.34, H.35, V.36, E.77, R.79 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.36, B:E.77 Salt bridges: B:H.35, B:R.79 SO4.18: 5 residues within 4Å: Chain C: H.155 Chain D: V.118, S.120, L.203, R.221 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.120, C:H.155 Salt bridges: D:R.221 SO4.19: 7 residues within 4Å: Chain A: H.185, G.186, W.188 Chain D: W.142, H.185, G.186, W.188 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.186, D:W.188, A:G.186, A:W.188 Salt bridges: D:H.185, A:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deuss, F.A. et al., Structural basis for the recognition of nectin-like protein-5 by the human-activating immune receptor, DNAM-1. J.Biol.Chem. (2019)

Release Date

2019-07-10

Peptides

CD226 antigen: AD
Poliovirus receptor: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
D

C
C

CD226 antigen

Poliovirus receptor

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