SMTL ID : 4h2s.1

Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.151, E.196, C.299 Ligands: PNS.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.151, A:E.196, A:C.299, H2O.8 ZN.3: 4 residues within 4Å: Chain B: C.151, E.196, C.299 Ligands: PNS.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.151, B:E.196, B:C.299, H2O.16

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 15 residues within 4Å: Chain A: 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 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.179, A:E.181, A:E.181, A:L.189, A:A.270, A:S.273, A:G.303 Water bridges: A:R.188, A:R.188, A:E.257, A:E.257 Salt bridges: A:R.179, A:K.255 pi-Stacking: A:F.192, A:F.192 pi-Cation interactions: A:R.306, A:R.306 AMP.4: 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 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.179, B:E.181, B:L.189, B:A.270, B:M.272, B:S.273, B:G.303 Water bridges: B:R.306, 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

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

ACT.5: 3 residues within 4Å: Chain B: K.98, T.284, W.285 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.98

2 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.6: 13 residues within 4Å: Chain A: Y.152, D.235, F.237, Q.249, Q.252, L.254, N.275, H.277, F.281, C.299 Chain C: T.61, S.62 Ligands: ZN.1 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.152, A:Q.249, A:Q.252, A:Q.252, A:H.277, C:S.62 PNS.7: 16 residues within 4Å: Chain B: F.105, Y.152, D.235, F.237, Q.249, Q.252, L.254, N.275, H.277, R.278, H.280, F.281, C.299 Chain D: T.61, S.62 Ligands: ZN.3 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:H.280 Hydrogen bonds: B:Q.249, B:Q.252, B:Q.252, D:S.62 Water bridges: B:S.104, B:Y.152 Salt bridges: B:R.278

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 1: 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 1

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