SMTL ID : 4bri.1

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG UMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

UNP.1: 20 residues within 4Å: Chain A: G.18, S.19, T.20, R.23, K.47, K.49, T.85, A.86, E.126, M.154, G.155, G.156, A.157, S.158, G.265, G.266, N.269, P.345, N.348 Ligands: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.19, A:S.19, A:T.20, A:T.20, A:R.23, A:R.23, A:R.23, A:K.47, A:K.49, A:K.49, A:T.85, A:T.85, A:A.86, A:M.154, A:G.156, A:A.157, A:S.158, A:G.266, A:N.269, A:P.345, A:N.348, A:L.349 Water bridges: A:D.16, A:D.16, A:G.155, A:Q.160, A:S.268, A:Q.347 Salt bridges: A:R.23 UNP.6: 20 residues within 4Å: Chain B: G.18, S.19, T.20, R.23, K.47, K.49, T.85, A.86, E.126, M.154, G.155, G.156, A.157, S.158, G.265, G.266, N.269, P.345, N.348 Ligands: MG.7 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:S.19, B:T.20, B:T.20, B:T.20, B:G.21, B:R.23, B:R.23, B:R.23, B:T.85, B:T.85, B:A.86, B:G.156, B:A.157, B:S.158, B:G.266, B:N.269, B:P.345, B:N.348 Water bridges: B:D.16, B:K.47, B:E.126, B:E.126, B:D.153, B:G.155, B:S.268, B:L.349 Salt bridges: B:R.23

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

MG.2: 1 residues within 4Å: Ligands: UNP.1 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: UNP.6 No protein-ligand interaction detected (PLIP)

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

MES.3: 9 residues within 4Å: Chain A: H.191, F.193, V.242, H.243, K.244, Q.248 Chain B: N.207, S.208, E.234 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.191, A:Q.248 Water bridges: A:L.194, A:V.242, A:H.243, A:H.243, B:Q.204, B:N.207, B:S.208 Salt bridges: A:H.243 MES.8: 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 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.248 Water bridges: B:H.191, B:L.194, B:L.194, B:V.242, B:H.243, B:Q.248, A:Q.204, A:Q.204 Salt bridges: B:H.191, B:H.243, A:E.234

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

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

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