SMTL ID : 4xqb.1

CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0461

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

1 x 425: 2-(1-{2-[bis(2-{4-[2-({(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl}oxy)ethyl]-1H-1,2,3-triazol-1-yl}ethyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)ethyl (6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranosidonic acid(Non-covalent)

425.1: 22 residues within 4Å: Chain A: Y.137, Y.141, P.146, P.149, V.151, S.173, K.174 Chain B: Y.137, Y.141, P.146, P.149, V.151, S.173, K.174 Chain C: Y.137, Y.141, P.146, D.147, P.149, V.151, S.173, K.174 35 PLIP interactions: 12 interactions with chain C, 11 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: C:Y.137, C:Y.141, C:P.146, C:V.151, A:Y.137, A:Y.141, A:P.146, A:V.151, B:Y.137, B:Y.141, B:P.146, B:V.151 Hydrogen bonds: C:Y.141, C:Y.141, C:P.146, C:S.173, C:S.173, A:Y.141, A:P.146, A:S.173, A:S.173, B:Y.141, B:P.146, B:S.173, B:S.173 Water bridges: C:T.139, C:S.173, A:T.139, A:S.173, B:T.139, B:K.174, B:K.174 Salt bridges: C:K.174, A:K.174, B:K.174

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.60, E.180 Ligands: ACT.8 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.60, A:E.180, H2O.1, ACT.8 ZN.3: 3 residues within 4Å: Chain A: K.65, E.177 Ligands: ACT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.177, A:E.177, ACT.4 ZN.5: 3 residues within 4Å: Chain A: C.42 Chain B: C.42 Chain C: C.42 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:C.42, A:C.42, C:C.42 ZN.9: 2 residues within 4Å: Chain B: H.60, E.180 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.60, B:E.180, H2O.12, H2O.12

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: E.177 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.65 ACT.6: 4 residues within 4Å: Chain A: I.27, A.28, K.58, Y.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.59 Water bridges: A:Y.59 Salt bridges: A:K.58 ACT.7: 4 residues within 4Å: Chain A: I.135, K.153 Chain C: G.143, G.144 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:G.143, A:K.130, A:Y.137 Salt bridges: A:K.130, A:K.153 ACT.8: 6 residues within 4Å: Chain A: V.55, H.60, E.180 Chain B: K.129, Y.131 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.131, B:Y.131 Salt bridges: B:K.129, A:H.60 ACT.10: 3 residues within 4Å: Chain B: K.124, T.160, C.162 3 PLIP interactions: 3 interactions with chain B Water bridges: B:C.162, B:C.162 Salt bridges: B:K.124 ACT.11: 4 residues within 4Å: Chain B: G.143, G.144 Chain C: I.135, K.153 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:G.143, C:K.130 Salt bridges: C:K.130, C:K.153 ACT.12: 3 residues within 4Å: Chain C: I.27, K.58, Y.59 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caraballo, R. et al., Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells. Org.Biomol.Chem. (2015)

Release Date

2015-07-29

Peptides

Fiber: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber

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