SMTL ID : 4h2w.1

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-oligomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.151, E.196, C.299 Ligands: PNS.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.151, A:E.196, A:C.299, H2O.7 ZN.4: 3 residues within 4Å: Chain B: C.151, E.196, C.299 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.151, B:E.196, B:E.196, B:C.299, H2O.8

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

CL.2: 7 residues within 4Å: Chain A: F.192, R.193, G.303, M.304, D.305, R.306 Ligands: 5GP.3 Ligand excluded by PLIP

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.3: 15 residues within 4Å: Chain A: R.179, D.187, R.188, L.189, F.192, M.194, K.255, A.270, C.271, M.272, S.273, A.301, G.303, R.306 Ligands: CL.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:L.189, A:D.235, A:D.235, A:A.270, A:S.273, A:S.273, A:G.303 Water bridges: A:K.255, A:K.255, A:D.305 Salt bridges: A:K.255 pi-Stacking: A:F.192, A:F.192 pi-Cation interactions: A:R.306, A:R.306

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 15 residues within 4Å: Chain B: R.179, E.181, D.187, R.188, L.189, F.192, M.194, K.255, A.270, C.271, M.272, S.273, A.301, G.303, R.306 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.181, B:L.189, B:A.270, B:S.273, B:G.303 Water bridges: B:R.179, B:S.273, B:R.306 Salt bridges: B:R.179, B:K.255 pi-Stacking: B:F.192, B:F.192 pi-Cation interactions: B:R.306, B:R.306

2 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.6: 11 residues within 4Å: Chain B: F.105, Y.152, D.235, F.237, N.248, Q.249, Q.252, L.254, H.277, H.280 Chain C: S.55 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.237 Hydrogen bonds: B:D.235, B:N.248, B:Q.249, B:Q.252 Water bridges: B:L.245 PNS.7: 13 residues within 4Å: Chain A: F.105, Y.152, D.235, N.248, Q.252, L.254, N.275, H.277, H.280 Chain D: S.55, F.56, R.80 Ligands: ZN.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:H.280, D:F.56 Hydrogen bonds: A:Y.152, A:D.235, A:N.248, A:Q.249, A:Q.252, A:Q.252, D:R.80 Water bridges: A:K.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mocibob, M. et al., Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation. Structure (2013)

Release Date

2013-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

Aminoacyl carrier protein

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