SMTL ID : 7cs0.1

Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Paromomycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x PAR: PAROMOMYCIN(Non-covalent)

PAR.1: 16 residues within 4Å: Chain A: F.42, D.54, F.55, D.59, E.106, A.107, S.141, A.142, S.143, I.145, D.177, S.180, D.208, W.210 Ligands: COA.2, CA.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.54, A:E.106, A:E.106, A:A.107, A:S.141, A:S.141, A:D.144, A:D.144, A:D.177, A:S.180, A:W.210 Water bridges: A:V.105, A:V.105, A:E.106, A:V.108, A:S.141, A:R.205 PAR.8: 17 residues within 4Å: Chain B: F.42, D.44, D.54, F.55, D.59, E.106, A.107, S.141, A.142, S.143, D.144, D.177, S.180, D.208, W.210 Ligands: COA.9, CA.11 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:D.54, B:E.106, B:A.107, B:S.141, B:S.141, B:D.144, B:D.177, B:S.180, B:D.208, B:W.210 Water bridges: B:D.59, B:V.105, B:V.105, B:E.106, B:E.106, B:V.108, B:S.141, B:S.180

2 x COA: COENZYME A(Non-covalent)

COA.2: 20 residues within 4Å: Chain A: A.41, F.42, V.108, A.109, V.110, R.115, G.116, D.117, G.118, L.119, G.120, T.121, A.142, S.143, A.146, P.148, M.149, Y.150, A.152 Ligands: PAR.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.42, A:V.110, A:R.115 Hydrogen bonds: A:V.110, A:G.116, A:G.116, A:G.118, A:L.119, A:G.120, A:T.121, A:T.121, A:T.121, A:S.143 Water bridges: A:D.117, A:D.117 COA.9: 18 residues within 4Å: Chain B: A.41, F.42, V.108, A.109, V.110, R.115, G.116, D.117, G.118, L.119, G.120, T.121, A.142, S.143, A.146, M.149, Y.150 Ligands: PAR.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.42, B:V.108, B:V.110 Hydrogen bonds: B:V.108, B:V.110, B:R.115, B:G.116, B:G.118, B:L.119, B:G.120, B:T.121, B:T.121, B:T.121 Water bridges: B:R.115, B:G.116, B:D.117

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

EDO.3: 3 residues within 4Å: Chain A: D.113, R.114, D.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.115 Water bridges: A:R.115 EDO.4: 6 residues within 4Å: Chain A: M.89, R.91, G.97, H.98 Chain B: P.167, W.204 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.91, A:R.91 Hydrogen bonds: B:W.204 EDO.10: 5 residues within 4Å: Chain A: P.167 Chain B: M.89, R.91, G.97, H.98 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.90, B:R.91, B:H.98, B:H.98

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

ACT.5: 6 residues within 4Å: Chain A: P.161, T.162, R.173, T.174, P.175, D.178 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.161, A:R.173 Hydrogen bonds: A:D.178 Salt bridges: A:R.173

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.6: 3 residues within 4Å: Chain A: D.54, D.59 Ligands: PAR.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:D.59, H2O.2, H2O.4 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 3 residues within 4Å: Chain B: D.54, D.59 Ligands: PAR.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.54, B:D.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeong, C.S. et al., Structural and biochemical analyses of an aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis. Sci Rep (2020)

Release Date

2021-06-23

Peptides

Aminoglycoside 2'-N-acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminoglycoside 2'-N-acetyltransferase

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