SMTL ID : 4xl8.1

Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with 2-O-Methyl-5-N-Acetylneuraminic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

2 x MNA: 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid(Non-covalent)

MNA.1: 7 residues within 4Å: Chain A: R.162, G.163, N.164 Chain B: G.149, E.150, N.154, Y.156 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.162, A:N.164, B:E.150 Water bridges: A:G.163, A:V.165, A:K.195 Salt bridges: A:R.162 MNA.6: 7 residues within 4Å: Chain A: S.148, G.149, N.154, Y.156 Chain C: R.162, G.163, N.164 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Water bridges: A:E.150, A:E.150, C:K.195 Hydrogen bonds: C:R.162, C:N.164 Salt bridges: C:R.162

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: I.40, Y.131, N.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.132

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.3: 3 residues within 4Å: Chain B: Y.56, A.91, E.92 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.56 Hydrogen bonds: B:Y.56, B:E.92 Water bridges: B:E.92

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 5 residues within 4Å: Chain B: A.144, R.145, G.146, G.147, E.150 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain B Hydrogen bonds: E.4, E.4, B:R.145, B:G.146, B:E.150 Water bridges: B:A.144

1 x ALA: ALANINE(Non-covalent)

ALA.5: 6 residues within 4Å: Chain B: G.105, K.106, L.107, F.117, S.118, Y.131 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:G.105, B:L.107, B:I.119, A.5, A.5

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

MPD.7: 5 residues within 4Å: Chain C: A.96, T.174, S.177, S.185, K.187 No protein-ligand interaction detected (PLIP)

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

MRD.8: 2 residues within 4Å: Chain C: A.179, T.180 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.179, C:T.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenman, A. et al., Human Adenovirus 52 Uses Sialic Acid-containing Glycoproteins and the Coxsackie and Adenovirus Receptor for Binding to Target Cells. Plos Pathog. (2015)

Release Date

2015-01-21

Peptides

Fiber-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber-1

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