SMTL ID : 5nc1.1

Structure of the distal domain of mouse adenovirus 2 fibre bound to N-acetyl-glucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 9 residues within 4Å: Chain A: N.97, Y.100, E.102, N.128, A.129, T.130, G.131, T.132, Q.133 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.97, A:N.97, A:E.102, A:E.102, A:T.130, A:T.132, A:Q.133 Water bridges: A:E.102, A:T.132 NAG.5: 9 residues within 4Å: Chain B: N.97, Y.100, E.102, N.128, A.129, T.130, G.131, T.132, Q.133 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.129 Hydrogen bonds: B:N.97, B:N.97, B:E.102, B:E.102, B:T.130, B:T.132, B:Q.133 Water bridges: B:T.132, B:T.132, B:T.132 NAG.12: 9 residues within 4Å: Chain C: N.97, Y.100, E.102, N.128, A.129, T.130, G.131, T.132, Q.133 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.97, C:N.97, C:E.102, C:E.102, C:T.130, C:T.132, C:Q.133 Water bridges: C:T.132

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

SO4.2: 6 residues within 4Å: Chain A: T.124, S.187, E.188, N.189, I.223 Chain C: Q.179 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.189, C:Q.179 Water bridges: A:S.187, A:G.190 SO4.3: 4 residues within 4Å: Chain A: Y.64, R.65, S.66, P.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.66, A:S.66 SO4.4: 4 residues within 4Å: Chain A: Y.85, S.145, M.151, P.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.85 Water bridges: A:C.146 SO4.6: 1 residues within 4Å: Chain B: R.96 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.96, B:T.99, B:T.99, B:N.101 Salt bridges: B:R.96 SO4.7: 3 residues within 4Å: Chain B: D.162, V.163, T.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.164, B:T.164, B:T.164 SO4.8: 1 residues within 4Å: Chain B: R.94 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.94 SO4.9: 3 residues within 4Å: Chain B: Y.204, R.205, L.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.204, B:L.206 Water bridges: B:G.207, B:G.207 SO4.10: 6 residues within 4Å: Chain A: L.118, S.227 Chain B: L.118, S.227 Chain C: L.118, S.227 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:S.227, A:S.227, B:S.227, C:S.227 SO4.13: 4 residues within 4Å: Chain C: Y.64, R.65, S.66, P.67 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.64, C:S.66 Salt bridges: C:R.65 SO4.14: 2 residues within 4Å: Chain C: F.46, T.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.47, C:T.47, C:T.47 SO4.15: 5 residues within 4Å: Chain C: Y.64, S.66, L.69, R.70, V.71 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.64, C:Y.64, C:V.71

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain B: N.97, G.98, T.99, Y.100, T.132, T.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.97, B:T.99, B:T.99, B:T.134, B:T.134

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre. J. Gen. Virol. (2018)

Release Date

2018-03-14

Peptides

Fiber: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber

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