SMTL ID : 3pzc.1

Crystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.151, E.196, C.299 Ligands: GAP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.151, A:E.196, A:C.299 ZN.5: 4 residues within 4Å: Chain B: C.151, E.196, C.299 Ligands: ACT.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.151, B:E.196, B:C.299

1 x GAP: GLYCYL-ADENOSINE-5'-PHOSPHATE(Non-covalent)

GAP.2: 21 residues within 4Å: Chain A: C.151, R.179, E.181, D.187, R.188, L.189, F.192, M.194, E.196, K.255, A.270, C.271, M.272, S.273, N.275, C.299, A.301, G.303, R.306 Ligands: ZN.1, GOL.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.181, A:E.181, A:L.189, A:D.235, A:A.270, A:M.272, A:S.273, A:G.303 Water bridges: A:R.179, A:K.255, A:E.257, A:R.306 Salt bridges: A:R.179, A:R.179, A:K.255, A:K.255 pi-Stacking: A:F.192, A:F.192 pi-Cation interactions: A:R.306, A:R.306

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.59, Y.63, E.64, V.67, R.193, D.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59, A:E.64, A:R.193 GOL.4: 6 residues within 4Å: Chain A: R.188, P.236, E.257, A.270, R.306 Ligands: GAP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.188, A:R.188, A:R.306, A:R.306 Water bridges: A:R.179

1 x COA: COENZYME A(Non-covalent)

COA.6: 16 residues within 4Å: Chain B: R.179, E.181, D.187, R.188, L.189, F.192, M.194, K.255, E.257, A.270, S.273, N.275, A.301, R.306 Ligands: ACT.8, ACT.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.179, B:L.189, B:S.273, B:N.275 Water bridges: B:P.148, B:A.270, B:A.270, B:R.306, B:R.306 Salt bridges: B:R.179, B:K.255, B:R.306, B:R.306 pi-Stacking: B:F.192, B:F.192 pi-Cation interactions: B:R.306, B:R.306

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

ACT.7: 4 residues within 4Å: Chain B: A.61, L.62, S.65, L.319 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.62, B:L.319 Hydrogen bonds: B:S.65 ACT.8: 9 residues within 4Å: Chain B: M.194, A.270, C.271, M.272, S.273, A.301, G.303, R.306 Ligands: COA.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.271, B:G.303 Salt bridges: B:R.306 ACT.9: 9 residues within 4Å: Chain B: A.149, C.151, Y.152, E.196, N.275, H.277, C.299 Ligands: ZN.5, COA.6 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.149 Salt bridges: B:H.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mocibob, M. et al., Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases. Croatica Chemica Acta (2011)

Release Date

2011-10-19

Peptides

Amino acid--[acyl-carrier-protein] ligase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amino acid--[acyl-carrier-protein] ligase 1

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