SMTL ID : 4brk.1

Legionella pneumophila NTPDase1 N302Y variant crystal form III (closed) in complex with MG UMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x UNP: 5'-O-[(R)-HYDROXY{[(S)-HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]OXY}PHOSPHORYL]URIDINE(Non-covalent)

UNP.1: 19 residues within 4Å: Chain A: G.18, S.19, T.20, R.23, T.85, A.86, E.126, M.154, G.155, G.156, A.157, S.158, Q.198, T.199, G.265, G.266, Y.269, Y.313 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.19, A:T.20, A:G.21, A:R.23, A:R.23, A:T.85, A:T.85, A:A.86, A:G.156, A:A.157, A:S.158, A:Q.198, A:T.199, A:G.266 Water bridges: A:G.155, A:Q.160, A:T.199, A:Y.269, A:Q.316 Salt bridges: A:R.23 pi-Stacking: A:Y.269, A:Y.313 UNP.8: 20 residues within 4Å: Chain B: G.18, S.19, T.20, G.21, R.23, T.85, A.86, E.126, M.154, G.155, G.156, A.157, S.158, Q.198, G.265, G.266, Y.269, Y.313 Ligands: MG.9, GOL.11 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.313 Hydrogen bonds: B:S.19, B:T.20, B:G.21, B:R.23, B:R.23, B:T.85, B:T.85, B:A.86, B:G.87, B:G.156, B:A.157, B:S.158, B:Q.198 Water bridges: B:D.16, B:G.155, B:Q.160, B:Y.269, B:Y.317, B:Y.317 Salt bridges: B:R.23 pi-Stacking: B:Y.269

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

MG.2: 1 residues within 4Å: Ligands: UNP.1 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: UNP.8 No protein-ligand interaction detected (PLIP)

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

MES.3: 6 residues within 4Å: Chain A: F.193, H.243, Q.248 Chain B: N.207, S.208, E.234 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.248 Water bridges: A:H.243, A:H.243, A:Q.248, B:Q.204 Salt bridges: A:H.243 MES.10: 9 residues within 4Å: Chain A: S.208, E.234 Chain B: H.191, S.192, F.193, V.242, H.243, K.244, Q.248 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.192, B:H.243, B:K.244, B:Q.248, B:Q.248 Water bridges: B:L.194 Salt bridges: B:H.191, B:H.243, A:E.234

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: G.265, S.268, Y.269, P.345, N.348, L.349 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.265, A:S.268, A:S.268, A:N.348, A:L.349 Water bridges: A:R.23, A:R.23, A:Y.269, A:Q.347 GOL.11: 7 residues within 4Å: Chain B: G.265, S.268, Y.269, P.345, N.348, L.349 Ligands: UNP.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.265, B:S.268, B:S.268, B:N.348, B:L.349 Water bridges: B:Y.269, B:P.345, B:Q.347

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

CL.5: 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.6: 5 residues within 4Å: Chain A: N.207, P.219, D.220 Chain B: R.89, G.123 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.89 Chain B: N.207, P.219, D.220 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