SMTL ID : 9fah.1

Human adenovirus type 37 fiber knob in complex with 4-O,5-N-diacetylneuraminic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x ANA: methyl 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

ANA.1: 9 residues within 4Å: Chain A: T.310, Y.312, P.317, D.318, P.320, K.345 Chain B: Y.308, V.322, S.344 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.312, A:P.317, B:Y.308 Hydrogen bonds: A:Y.312, A:P.317, A:P.317, B:S.344 Salt bridges: A:K.345 ANA.9: 7 residues within 4Å: Chain B: Y.312, P.317, D.318, P.320, K.345 Chain C: Y.308, V.322 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.312, B:P.317, C:Y.308 Hydrogen bonds: B:Y.312, B:P.317 Water bridges: B:K.345 Salt bridges: B:K.345 ANA.13: 9 residues within 4Å: Chain A: Y.308, V.322, S.344 Chain C: T.310, Y.312, P.317, D.318, P.320, K.345 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:Y.308, C:T.310, C:Y.312, C:P.317 Hydrogen bonds: A:S.344, C:Y.312, C:P.317 Salt bridges: C:K.345

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.231 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.231 ZN.3: 4 residues within 4Å: Chain A: K.212, G.214, E.365 Ligands: ACT.15 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.365, A:E.365, H2O.4, ACT.15 ZN.4: 2 residues within 4Å: Chain A: E.351 Ligands: ACT.5 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.351, A:E.351, H2O.4, ACT.5 ZN.10: 2 residues within 4Å: Chain B: H.231 Ligands: CL.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.231, H2O.7, H2O.11 ZN.14: 4 residues within 4Å: Chain C: V.225, H.231, E.351, E.353 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.231, C:E.351, H2O.8

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

ACT.5: 5 residues within 4Å: Chain A: E.351 Chain B: K.300, K.301, Y.302 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.302 ACT.6: 2 residues within 4Å: Chain A: N.251, K.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.252 ACT.7: 2 residues within 4Å: Chain A: K.316, D.318 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.319 Salt bridges: A:K.316 ACT.8: 4 residues within 4Å: Chain A: A.283, I.284, G.285, E.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.284, A:G.285 ACT.11: 3 residues within 4Å: Chain B: K.316, D.318, Q.319 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.316 Hydrogen bonds: B:Q.319 ACT.15: 6 residues within 4Å: Chain A: K.212, G.214, E.365 Chain C: D.182, R.270 Ligands: ZN.3 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Salt bridges: C:K.180, C:R.270, A:K.212 Water bridges: A:K.212 ACT.16: 3 residues within 4Å: Chain C: K.316, D.318, Q.319 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.319 Salt bridges: C:K.316 ACT.17: 3 residues within 4Å: Chain C: Q.200, A.227, G.228 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.200, C:G.228

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain B: H.231, E.351 Chain C: K.300 Ligands: ZN.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liaci, A.M. et al., Extended receptor repertoire of an adenovirus associated with human obesity. Plos Pathog. (2025)

Release Date

2025-01-22

Peptides

Fiber: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fiber