SMTL ID : 6g47.1

Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with alpha-(2,8)-Trisialic Acid (DP3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

1 x SIA- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA-SIA.1: 8 residues within 4Å: Chain A: S.148, G.149, N.154, Y.156 Chain C: R.162, G.163, N.164, E.194 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.162, C:N.164 Water bridges: C:K.195, C:K.195, C:K.195, A:E.150 Salt bridges: C:R.162

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

SIA.2: 8 residues within 4Å: Chain A: R.162, G.163, N.164 Chain B: S.148, G.149, P.151, N.154, Y.156 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.162, A:N.164 Water bridges: A:G.163, A:V.165, A:K.195, A:K.195 Salt bridges: A:R.162

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 13 residues within 4Å: Chain A: L.75, Y.155, S.202, F.203 Chain B: L.75, S.202, F.203, C.204 Chain C: L.75, Y.155, S.202, F.203, C.204 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.155, A:Y.155 Water bridges: C:Y.155 Hydrophobic interactions: A:L.75 MPD.7: 7 residues within 4Å: Chain B: R.162, G.163 Chain C: S.148, G.149, P.151, N.154, Y.156 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.162 Water bridges: C:Y.156

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 2 residues within 4Å: Chain B: E.92, S.94 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.94 Water bridges: B:T.93 MRD.5: 4 residues within 4Å: Chain B: R.167, P.168, T.189, V.191 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.189, B:V.191 Hydrogen bonds: B:R.167

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 4 residues within 4Å: Chain C: V.55, Y.56, L.95, A.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenman, A. et al., Polysialic acid is a cellular receptor for human adenovirus 52. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-02

Peptides

Fiber-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber-1

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