SMTL ID : 4brn.2 (1 other biounit)

Legionella pneumophila NTPDase1 crystal form III (closed) in complex with Mg AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 12 residues within 4Å: Chain A: G.18, S.19, T.20, R.23, M.154, G.155, G.156, Q.198, G.266, N.269, Y.313 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.19, A:T.20, A:G.21, A:G.155, A:G.156, A:Q.198 Water bridges: A:D.16, A:D.16, A:A.157, A:G.266, A:G.266 Salt bridges: A:R.23 pi-Stacking: A:Y.313, A:Y.313 AMP.7: 16 residues within 4Å: Chain B: G.18, S.19, T.20, R.23, M.154, G.155, G.156, Q.198, G.266, N.269, L.270, Y.313, Y.317, L.320, Y.324 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.19, B:T.20, B:G.21, B:G.155, B:G.156, B:Q.198, B:Y.317, B:Y.324 Water bridges: B:D.16, B:T.85, B:T.85, B:T.85, B:A.157 Salt bridges: B:R.23 pi-Stacking: B:Y.313, B:Y.313

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.23, E.126 Ligands: AMP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: F.107, Q.110, W.113 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.107, A:Q.110, A:W.113, H2O.3 MG.8: 2 residues within 4Å: Chain B: R.23 Ligands: AMP.7 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.7, H2O.7, H2O.8, H2O.9, H2O.10, AMP.7

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

CL.3: 5 residues within 4Å: Chain A: R.89, G.123 Chain B: N.207, P.219, D.220 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: I.55, Q.56, T.61 Chain B: I.55, Q.56, T.61 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: N.207, P.219, D.220 Chain B: R.89 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zebisch, M. et al., Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases. Structure (2013)

Release Date

2013-07-17

Peptides

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I

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