SMTL ID : 3zeu.2 (1 other biounit)

Structure of a Salmonella typhimurium YgjD-YeaZ heterodimer bound to ATPgammaS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-oligomer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: A.108, T.109, R.110 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain B: R.326, P.327, R.328 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: W.224 Chain B: V.43, P.44, E.45 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain B: H.111, H.115, D.300 Ligands: AGS.6, ADP.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.111, B:H.115, B:D.300

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain B: D.11, E.12 Ligands: ADP.7 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.11, B:E.12, H2O.8, H2O.8, H2O.8, H2O.8 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.6: 22 residues within 4Å: Chain B: H.111, M.112, H.115, S.136, G.137, G.138, H.139, G.163, F.166, D.167, G.180, P.181, G.267, G.268, V.269, A.271, N.272, C.298, T.299, D.300 Ligands: ZN.3, ADP.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.136, B:G.137, B:G.138, B:H.139, B:H.139, B:D.167, B:G.180, B:G.268, B:N.272, B:D.300 Water bridges: B:S.184, B:S.184 Salt bridges: B:H.115 pi-Stacking: B:F.166

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.7: 22 residues within 4Å: Chain B: H.111, H.115, S.136, G.137, G.138, G.163, E.164, F.166, D.167, G.180, P.181, G.267, G.268, V.269, A.271, N.272, C.298, T.299, D.300 Ligands: ZN.3, MG.4, AGS.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.137, B:G.138, B:D.167, B:G.180, B:G.268, B:N.272, B:D.300 Water bridges: B:S.184, B:S.184 Salt bridges: B:H.115 pi-Stacking: B:F.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nichols, C.E. et al., Crystal Structure of the Dimer of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz and Calorimetric Evidence for the Formation of a Ternary Ygjd-Yeaz-Yjee Complex. Protein Sci. (2013)

Release Date

2013-03-20

Peptides

PUTATIVE M22 PEPTIDASE YEAZ: A
PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PUTATIVE M22 PEPTIDASE YEAZ

PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP

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