SMTL ID : 4h2v.1

Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with glycylated carrier protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: H2V.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.151, A:E.196, A:C.299 ZN.6: 3 residues within 4Å: Chain B: C.151, E.196, C.299 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.151, B:E.196, B:C.299, H2O.325

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 16 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 Ligands: H2V.12 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.179, A:E.181, A:L.189, A:A.270, A:S.273, A:G.303 Water bridges: A:R.188, A:R.188, A:D.235, A:D.235, A:E.257, A:E.257, A:R.306 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.7: 16 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 Ligands: PO4.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.179, B:E.181, B:L.189, B:A.270, B:S.273, B:G.303 Water bridges: B:R.188, B:R.188, 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

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

ACT.3: 1 residues within 4Å: Chain A: R.78 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.78 ACT.4: 4 residues within 4Å: Chain A: S.76, H.77, R.78, R.216 No protein-ligand interaction detected (PLIP) ACT.5: 2 residues within 4Å: Chain A: H.49, S.50 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.50 Water bridges: A:H.49, B:S.160, B:S.160 Salt bridges: A:H.49

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain B: E.121, T.137, S.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.138 Water bridges: B:R.128, B:S.138 SO4.9: 3 residues within 4Å: Chain B: S.183, H.185, R.188 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.183, B:S.183 Water bridges: B:K.184, B:H.185 Salt bridges: B:H.185, B:R.188

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.10: 3 residues within 4Å: Chain B: R.188, R.306 Ligands: AMP.7 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.179, B:R.188, B:R.188, B:E.257, B:E.257, B:R.306 Salt bridges: B:R.188, B:R.306

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 2 residues within 4Å: Chain B: H.49, S.50 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:S.160, B:H.49, B:H.49 Hydrogen bonds: B:S.50

1 x H2V: S-[2-({N-[(2S)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL] AMINOETHANETHIOATE(Covalent)

H2V.12: 17 residues within 4Å: Chain A: A.149, C.151, Y.152, E.196, D.235, F.237, K.245, Q.249, Q.252, N.275, H.277, C.299 Chain C: T.61, S.62, M.63 Ligands: ZN.1, AMP.2 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:S.62, A:E.196, A:K.245, A:K.245, A:Q.249, A:Q.252 Hydrophobic interactions: A:K.245, A:Q.249 Water bridges: A:Y.152, A:Y.152, A:K.255

1 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.13: 12 residues within 4Å: Chain B: Y.152, D.235, F.237, Q.249, Q.252, N.275, H.277, H.280, F.281, C.299 Chain D: T.61, S.62 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.249, B:Q.252, D:S.62 Water bridges: B:D.235, B: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 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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