SMTL ID : 7q1d.1 (1 other biounit)

Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 1 residues within 4Å: Chain A: D.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.69, A:D.69 Water bridges: A:Q.65 NA.2: 1 residues within 4Å: Chain A: E.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.175 NA.3: 1 residues within 4Å: Chain A: E.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.175 Water bridges: A:A.173

2 x 8I8: [[(2~{R},3~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[(3~{S})-3-[2-[(1~{S})-1-[[(1~{S},2~{R},3~{R},4~{S},5~{R})-5-azanyl-3-[(4~{S},5~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{E})-3-azanyl-6-(azanylmethylidene)-4,5-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)-3-oxidanyl-oxolan-2-yl]oxy-2-[(2~{S},3~{R},4~{R},5~{S})-3-azanyl-6-(iminomethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-cyclohexyl]amino]-1-oxidanyl-ethyl]sulfanylethylamino]-3-oxidanyl-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate(Non-covalent)

8I8.4: 27 residues within 4Å: Chain A: H.47, A.48, S.49, V.50, K.51, P.60, Y.80, E.118, N.119, S.120, V.121, F.125, E.139, Y.162, A.183, P.184, D.186, T.187, I.188, T.189, H.192, T.228, G.229, D.230, F.237 Chain B: R.114, R.117 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.48, A:A.48, A:V.50, A:K.51, A:Y.80, A:V.121, A:E.139, A:E.139, A:D.186, A:G.229, A:D.230, B:R.117 Water bridges: A:A.48, A:S.49, A:S.49, A:E.118, A:E.118, A:N.119, A:D.186, A:D.186, A:D.186 Salt bridges: A:K.51, B:R.117 8I8.7: 27 residues within 4Å: Chain A: R.114, R.117 Chain B: H.47, A.48, S.49, V.50, K.51, P.60, Y.80, E.118, N.119, S.120, V.121, F.125, E.139, Y.162, A.183, P.184, D.186, T.187, I.188, T.189, H.192, T.228, G.229, D.230, F.237 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.48, B:A.48, B:V.50, B:K.51, B:Y.80, B:V.121, B:E.139, B:E.139, B:D.186, B:D.186, B:D.230, A:R.117 Water bridges: B:L.46, B:S.49, B:S.49, B:E.118, B:N.119, B:N.119, B:D.186, B:D.186, A:Q.84, A:A.115 Salt bridges: B:K.51, A:R.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.91, K.98, L.102, W.220, V.221, T.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.98, A:K.98, A:V.221 Water bridges: A:T.222

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

CL.6: 2 residues within 4Å: Chain B: R.217, K.218 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pontillo, N. et al., 3-N-alkylation in aminoglycoside antibiotic neomycin B overcomes bacterial resistance mediated by acetyltransferase (3) IIIa. To Be Published

Release Date

2022-11-02

Peptides

Aminoglycoside N(3)-acetyltransferase III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Aminoglycoside N(3)-acetyltransferase III

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