- 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)
- 2 x COA: COENZYME A(Non-covalent)
COA.3: 21 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, N.136, L.139, F.192, N.194, V.212, L.214, V.226, P.227
- Ligands: 9CS.2
17 PLIP interactions:10 interactions with chain A, 7 interactions with chain B- Hydrophobic interactions: A:I.206, A:V.224, B:F.192
- Hydrogen bonds: A:Y.186, A:A.189, A:S.209, A:S.209, B:A.135, B:N.136, B:N.194
- Water bridges: A:S.209, A:S.209, B:H.134, B:N.136, B:N.136
- Salt bridges: A:K.231, A:R.232
COA.13: 23 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, K.169, F.192, N.194, V.212, L.214, V.226, P.227
- Ligands: 9CS.12
14 PLIP interactions:7 interactions with chain C, 7 interactions with chain B- Hydrophobic interactions: C:F.192, B:Y.186
- 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: C:N.136, C:N.136
- Salt bridges: C:K.169, B:K.231, B:R.232
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 4 residues within 4Å:- Chain A: L.139, K.169
- Chain C: K.231, R.232
5 PLIP interactions:2 interactions with chain C, 3 interactions with chain A- Hydrogen bonds: C:K.231, C:K.231, A:K.169
- Water bridges: A:N.136, A:N.136
EDO.5: 3 residues within 4Å:- Chain A: R.13, F.90, E.91
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:R.13, A:R.13
- Water bridges: A:P.89, A:E.91, A:R.101
EDO.6: 3 residues within 4Å:- Chain A: R.13, Y.14, N.76
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.13, A:Y.14
- Water bridges: A:Y.14, A:N.76
EDO.7: 7 residues within 4Å:- Chain A: Q.149, F.160, Q.161, L.164, Y.172, Y.174
- Ligands: SO4.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.149, A:Q.161
- Water bridges: A:Q.149
EDO.9: 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.10: 5 residues within 4Å:- Chain B: Q.149, Q.161, L.164, Y.172, Y.174
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.149, B:Q.161
EDO.14: 6 residues within 4Å:- Chain C: Q.149, F.160, Q.161, L.164, Y.172, Y.174
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Q.149, C:Q.161, C:Q.161
- Water bridges: C:Y.174, C:Y.174
- 3 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 2 residues within 4Å:- Ligands: 9CS.1, EDO.7
3 PLIP interactions:3 interactions with chain A- Water bridges: A:D.146, A:Q.149, A:N.150
SO4.11: 1 residues within 4Å:- Ligands: 9CS.2
6 PLIP interactions:6 interactions with chain B- Water bridges: B:D.146, B:D.146, B:D.147, B:D.147, B:D.147, B:N.150
SO4.15: 1 residues within 4Å:- Ligands: 9CS.12
1 PLIP interactions:1 interactions with chain C- Water bridges: C:Q.149
- 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
CB
FC
E
- 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)
- 2 x COA: COENZYME A(Non-covalent)
- 7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- 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
CB
FC
E