SMTL ID : 4brq.1

LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 12 residues within 4Å: Chain A: T.20, R.23, K.47, G.156, Q.198, G.266, N.269, L.270, Y.313, Y.317, L.320 Ligands: PO4.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.20, A:Q.198, A:N.269, A:Y.317 Water bridges: A:R.23, A:M.154, A:G.266, A:G.266, A:Y.313, A:Y.313 Salt bridges: A:R.23, A:K.47 pi-Stacking: A:Y.313, A:Y.313 AMP.8: 12 residues within 4Å: Chain B: T.20, R.23, K.47, G.156, Q.198, G.266, N.269, L.270, Y.313, Y.317, L.320 Ligands: PO4.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.198, B:Y.317 Water bridges: B:T.20, B:R.23, B:K.49, B:K.49, B:M.154, B:G.266, B:G.266, B:Y.313 Salt bridges: B:R.23, B:K.47, B:K.49 pi-Stacking: B:Y.313, B:Y.313

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 11 residues within 4Å: Chain A: H.191, S.192, F.193, L.194, V.242, H.243, K.244, Q.248 Chain B: N.207, S.208, E.234 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:S.208 Salt bridges: B:E.234, A:H.191, A:H.243 Hydrogen bonds: A:S.192, A:L.194, A:H.243, A:Q.248, A:Q.248 MES.9: 9 residues within 4Å: Chain A: N.207, S.208, E.234 Chain B: H.191, S.192, F.193, V.242, H.243, Q.248 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.243, B:H.243, B:Q.248 Water bridges: B:K.244, A:S.208 Salt bridges: B:H.191, B:H.243, A:E.234

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

PO4.3: 10 residues within 4Å: Chain A: G.18, S.19, T.20, G.21, R.23, G.155, G.156 Ligands: AMP.1, PO4.4, MG.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.19, A:T.20, A:T.20, A:G.21, A:G.156, A:A.157 Water bridges: A:G.266, A:G.266 Salt bridges: A:R.23 PO4.4: 11 residues within 4Å: Chain A: T.85, A.86, R.89, E.126, G.155, G.156, A.157, S.158, Q.160 Ligands: PO4.3, MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.19, A:T.85, A:A.86, A:R.89, A:G.155, A:G.156, A:A.157, A:S.158, A:S.158, A:S.158, A:Q.160 PO4.10: 10 residues within 4Å: Chain B: G.18, S.19, T.20, G.21, R.23, G.155, G.156 Ligands: AMP.8, PO4.11, MG.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.19, B:S.19, B:T.20, B:T.20, B:G.21, B:G.156 Water bridges: B:G.266 Salt bridges: B:R.23 PO4.11: 10 residues within 4Å: Chain B: T.85, A.86, E.126, G.155, G.156, A.157, S.158, Q.160 Ligands: PO4.10, MG.12 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.19, B:S.19, B:A.86, B:R.89, B:E.126, B:G.156, B:A.157, B:S.158, B:Q.160 Water bridges: B:E.126, B:E.126, B:E.126

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

CL.5: 5 residues within 4Å: Chain A: N.207, P.219, D.220 Chain B: R.89, G.123 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: R.89, G.123 Chain B: N.207, P.219, D.220 Ligand excluded by PLIP

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

MG.6: 2 residues within 4Å: Ligands: PO4.3, PO4.4 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: R.23 Ligands: PO4.10, PO4.11 No protein-ligand interaction detected (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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