SMTL ID : 6qu6.1

Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH4.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-trimer

Ligands

3 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.1: 11 residues within 4Å: Chain A: I.148, S.149, N.150, I.162, Q.186 Chain C: Y.152, T.157, Y.158, P.160, K.187 Ligands: SLB.2 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.152, C:P.160, A:I.162 Hydrogen bonds: C:Y.152, C:Y.152, C:T.157, C:K.187, A:N.150 Water bridges: C:N.150 Salt bridges: C:K.187 SIA.7: 11 residues within 4Å: Chain A: Y.152, T.157, Y.158, P.160, K.187 Chain B: I.148, S.149, N.150, I.162, Q.186 Ligands: SLB.8 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.152, A:P.160, B:I.162 Hydrogen bonds: A:Y.152, A:Y.152, A:T.157, A:K.187, B:N.150 Water bridges: A:N.150 Salt bridges: A:K.187 SIA.13: 11 residues within 4Å: Chain B: Y.152, T.157, Y.158, P.160, K.187 Chain C: I.148, S.149, N.150, I.162, Q.186 Ligands: SLB.14 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.152, B:P.160, C:I.162 Hydrogen bonds: B:Y.152, B:Y.152, B:T.157, B:K.187, C:N.150 Water bridges: B:N.150 Salt bridges: B:K.187

3 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.2: 12 residues within 4Å: Chain A: I.148, S.149, N.150, I.162, W.185, Q.186 Chain C: Y.152, T.157, Y.158, P.160, K.187 Ligands: SIA.1 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.152, C:P.160, A:I.162 Hydrogen bonds: C:Y.152, C:Y.152, C:T.157, C:K.187, A:N.150 Water bridges: C:N.150, A:I.162, A:T.184 Salt bridges: C:K.187 SLB.8: 12 residues within 4Å: Chain A: Y.152, T.157, Y.158, P.160, K.187 Chain B: I.148, S.149, N.150, I.162, W.185, Q.186 Ligands: SIA.7 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.152, A:P.160, B:I.162 Hydrogen bonds: A:Y.152, A:Y.152, A:T.157, A:K.187, B:N.150 Water bridges: A:N.150, B:I.162, B:T.184 Salt bridges: A:K.187 SLB.14: 12 residues within 4Å: Chain B: Y.152, T.157, Y.158, P.160, K.187 Chain C: I.148, S.149, N.150, I.162, W.185, Q.186 Ligands: SIA.13 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:I.162, B:Y.152, B:P.160 Hydrogen bonds: C:N.150, B:Y.152, B:Y.152, B:T.157, B:K.187 Water bridges: C:I.162, C:T.184, B:N.150 Salt bridges: B:K.187

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

SO4.3: 2 residues within 4Å: Chain A: K.79, K.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.80 Water bridges: A:K.80, A:K.80 Salt bridges: A:K.79, A:K.80 SO4.9: 2 residues within 4Å: Chain B: K.79, K.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.80 Water bridges: B:K.80, B:K.80 Salt bridges: B:K.79, B:K.80 SO4.15: 2 residues within 4Å: Chain C: K.79, K.80 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.80 Water bridges: C:K.80, C:K.80 Salt bridges: C:K.79, C:K.80

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

EDO.4: 4 residues within 4Å: Chain A: K.79, D.81, K.83, T.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.81 EDO.5: 8 residues within 4Å: Chain A: S.198, F.199, T.200 Chain B: I.147, F.199, F.201 Ligands: EDO.11, EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.200, A:T.200, A:T.200 EDO.10: 4 residues within 4Å: Chain B: K.79, D.81, K.83, T.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.81 EDO.11: 8 residues within 4Å: Chain B: S.198, F.199, T.200 Chain C: I.147, F.199, F.201 Ligands: EDO.5, EDO.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.200, B:T.200, B:T.200 EDO.16: 4 residues within 4Å: Chain C: K.79, D.81, K.83, T.182 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.81 EDO.17: 8 residues within 4Å: Chain A: I.147, F.199, F.201 Chain C: S.198, F.199, T.200 Ligands: EDO.5, EDO.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.200, C:T.200, C:T.200

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain A: A.155, L.156, T.157, Y.158 Chain B: I.148, T.164, T.182, T.184 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.155, A:T.157, B:T.164 Water bridges: A:T.157, B:K.146, B:T.164 PEG.12: 8 residues within 4Å: Chain B: A.155, L.156, T.157, Y.158 Chain C: I.148, T.164, T.182, T.184 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:T.164, B:A.155, B:T.157 Water bridges: C:K.146, C:T.164, B:T.157 PEG.18: 8 residues within 4Å: Chain A: I.148, T.164, T.182, T.184 Chain C: A.155, L.156, T.157, Y.158 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:A.155, C:T.157, A:T.164 Water bridges: C:T.157, A:K.146, A:T.164

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Baker, A.T. et al., Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor. Sci Adv (2019)

Release Date

2019-09-18

Peptides

Fiber: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Fiber

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