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

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with kanamycin B and coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-trimer

Ligands

3 x 9CS: (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE(Non-covalent)

9CS.1: 16 residues within 4Å: Chain A: D.83, G.86, E.87, Y.104, F.105, G.106, G.129 Chain B: N.115, Y.117, H.134, H.137, D.146, D.147, Y.172 Ligands: COA.2, SO4.9 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:N.115, B:N.115, B:Y.117, B:H.137, B:D.147, A:Y.104, A:F.105, A:F.105 Salt bridges: B:H.134 Water bridges: A:D.57, A:D.83, A:D.83, A:G.85, A:D.107 9CS.6: 16 residues within 4Å: Chain B: D.83, G.86, E.87, Y.104, F.105, G.106, G.129 Chain C: N.115, Y.117, H.137, D.146, D.147, Y.172 Ligands: COA.7, SO4.11, SO4.15 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:N.115, C:N.115, C:Y.117, C:Y.117, C:H.137, C:D.147, B:Y.104, B:F.105, B:F.105 Water bridges: C:D.146, C:D.146, B:G.85, B:E.87, B:E.87 Salt bridges: C:H.134 9CS.12: 16 residues within 4Å: Chain A: N.115, Y.117, H.134, H.137, D.146, D.147, Y.172 Chain C: D.83, G.86, E.87, Y.104, F.105, G.106, G.129 Ligands: SO4.4, COA.13 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:N.115, A:Y.117, A:Y.117, A:H.137, A:D.147, C:Y.104, C:Y.104, C:F.105, C:F.105 Water bridges: A:N.115, A:N.115, A:H.134, A:H.134, C:G.85, C:E.87, C:E.87, C:D.107 Salt bridges: A:H.134

3 x COA: COENZYME A(Non-covalent)

COA.2: 22 residues within 4Å: Chain A: N.128, Y.186, I.187, G.188, A.189, I.206, G.208, S.209, V.224, K.231, R.232 Chain B: H.134, A.135, N.136, L.139, F.192, N.194, V.212, L.214, V.226, P.227 Ligands: 9CS.1 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:A.189, A:S.209, A:S.209, B:N.136, B:N.136, B:N.194 Water bridges: A:G.225, A:R.232, A:R.232, B:K.169, B:K.169, B:K.169 Salt bridges: A:K.231, A:R.232 Hydrophobic interactions: B:F.192 COA.7: 22 residues within 4Å: Chain B: N.128, Y.186, I.187, G.188, A.189, I.206, G.208, S.209, V.224, K.231, R.232 Chain C: H.134, A.135, N.136, L.139, F.192, N.194, V.212, L.214, V.226, P.227 Ligands: 9CS.6 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:F.192, B:I.206 Hydrogen bonds: C:A.135, C:N.136, C:N.194, B:Y.186, B:A.189, B:S.209, B:S.209 Water bridges: B:K.231 Salt bridges: B:K.231, B:R.232 COA.13: 21 residues within 4Å: Chain A: H.134, A.135, N.136, L.139, F.192, N.194, V.212, L.214, V.226 Chain C: N.128, Y.186, I.187, G.188, A.189, I.206, G.208, S.209, V.224, K.231, R.232 Ligands: 9CS.12 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:F.192, C:I.206 Hydrogen bonds: A:N.136, A:N.194, C:Y.186, C:Y.186, C:A.189, C:S.209, C:S.209 Water bridges: A:H.134, A:N.136, A:R.229 Salt bridges: C:R.232

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: W.251, E.255, N.259, K.272, Y.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.255, A:K.272, A:K.272 EDO.8: 2 residues within 4Å: Chain B: R.13, Y.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.13, B:Y.14 EDO.14: 4 residues within 4Å: Chain C: W.251, E.255, N.259, Y.273 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.255, C:E.255, C:N.259, C:Y.273

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

SO4.4: 3 residues within 4Å: Chain A: D.146, D.147 Ligands: 9CS.12 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.147, A:D.147, A:N.150 SO4.5: 2 residues within 4Å: Chain A: R.13, Y.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.13 Salt bridges: A:R.13 SO4.9: 1 residues within 4Å: Ligands: 9CS.1 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.149, B:Q.149, B:Q.149 SO4.10: 5 residues within 4Å: Chain B: Q.149, F.160, Q.161, Y.172, Y.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.149, B:Q.161 SO4.11: 4 residues within 4Å: Chain B: G.106, D.107, G.129 Ligands: 9CS.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.107, B:G.129 Water bridges: B:D.107, B:G.108, B:G.108 SO4.15: 1 residues within 4Å: Ligands: 9CS.6 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.147, C:D.147

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

CL.16: 3 residues within 4Å: Chain C: R.13, F.90, E.91 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bordeleau, E. et al., Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat.Chem.Biol. (2024)

Release Date

2022-11-02

Peptides

Aminocyclitol acetyltransferase ApmA: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Aminocyclitol acetyltransferase ApmA

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