SMTL ID : 6qu8.1

Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH8.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

homo-trimer

Ligands

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

SIA.1: 10 residues within 4Å: Chain A: I.148, N.150, I.162, Q.186 Chain B: Y.152, T.157, Y.158, P.160, K.187 Ligands: SLB.2 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.148, A:I.162, B:Y.152, B:P.160 Hydrogen bonds: A:N.150, A:Q.186, B:T.157 Water bridges: B:N.150, B:Y.152 Salt bridges: B:K.187 SIA.6: 10 residues within 4Å: Chain B: I.148, N.150, I.162, Q.186 Chain C: Y.152, T.157, Y.158, P.160, K.187 Ligands: SLB.7 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.148, B:I.162, C:Y.152, C:P.160 Hydrogen bonds: B:N.150, B:Q.186, C:T.157 Water bridges: C:N.150, C:Y.152 Salt bridges: C:K.187 SIA.11: 10 residues within 4Å: Chain A: Y.152, T.157, Y.158, P.160, K.187 Chain C: I.148, N.150, I.162, Q.186 Ligands: SLB.12 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.152, A:P.160, C:I.148, C:I.162 Hydrogen bonds: A:T.157, C:N.150, C:Q.186 Water bridges: A:N.150, A:Y.152 Salt bridges: A:K.187

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

SLB.2: 10 residues within 4Å: Chain A: I.148, N.150, I.162, Q.186 Chain B: Y.152, T.157, Y.158, P.160, K.187 Ligands: SIA.1 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.148, A:I.162, B:Y.152, B:P.160 Hydrogen bonds: A:N.150, A:Q.186, B:T.157, B:K.187, B:K.187 Water bridges: B:N.150, B:Y.152 Salt bridges: B:K.187 SLB.7: 10 residues within 4Å: Chain B: I.148, N.150, I.162, Q.186 Chain C: Y.152, T.157, Y.158, P.160, K.187 Ligands: SIA.6 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:I.148, B:I.162, C:Y.152, C:P.160 Hydrogen bonds: B:N.150, B:Q.186, C:T.157, C:K.187, C:K.187 Water bridges: C:N.150, C:Y.152 Salt bridges: C:K.187 SLB.12: 10 residues within 4Å: Chain A: Y.152, T.157, Y.158, P.160, K.187 Chain C: I.148, N.150, I.162, Q.186 Ligands: SIA.11 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Y.152, A:P.160, C:I.148, C:I.162 Hydrogen bonds: A:T.157, A:K.187, A:K.187, C:N.150, C:Q.186 Water bridges: A:N.150, A:Y.152 Salt bridges: A:K.187

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

EDO.3: 6 residues within 4Å: Chain A: K.140, N.141, S.143 Chain B: G.154, Q.193, D.195 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.141, B:Q.193, B:D.195 Water bridges: B:Q.193 EDO.4: 4 residues within 4Å: Chain A: D.81, K.83, T.182, T.184 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.81, A:D.81 EDO.5: 5 residues within 4Å: Chain A: K.38, M.39, K.83, I.84, S.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.39, A:S.99 Water bridges: A:K.83, A:S.99 EDO.8: 6 residues within 4Å: Chain B: K.140, N.141, S.143 Chain C: G.154, Q.193, D.195 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.193, B:N.141 Water bridges: C:Q.193 EDO.9: 4 residues within 4Å: Chain B: D.81, K.83, T.182, T.184 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.81, B:D.81 EDO.10: 5 residues within 4Å: Chain B: K.38, M.39, K.83, I.84, S.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.39, B:S.99 Water bridges: B:K.83, B:S.99 EDO.13: 6 residues within 4Å: Chain A: G.154, Q.193, D.195 Chain C: K.140, N.141, S.143 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.193, A:D.195, C:N.141 Water bridges: A:Q.193 EDO.14: 4 residues within 4Å: Chain C: D.81, K.83, T.182, T.184 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.81, C:D.81 EDO.15: 5 residues within 4Å: Chain C: K.38, M.39, K.83, I.84, S.99 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:M.39, C:S.99 Water bridges: C:K.83, C:S.99

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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