SMTL ID : 2woe.1 (2 other biounits)

Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.33, D.248, D.250, T.251 Ligands: AR6.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.33, A:D.248, A:D.250, A:D.250, A:T.251

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.2: 22 residues within 4Å: Chain A: E.33, D.65, N.102, V.103, G.104, N.105, T.106, C.107, E.126, G.127, A.129, G.130, N.131, G.132, M.135, H.163, A.216, Y.217, D.248, D.250, T.251 Ligands: MN.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.65, A:N.102, A:N.105, A:N.105, A:T.106, A:T.106, A:C.107, A:E.126, A:A.129, A:G.132 Water bridges: A:E.126, A:D.128, A:G.130, A:Y.217, A:Y.217 Salt bridges: A:H.163 pi-Stacking: A:Y.217

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 2 residues within 4Å: Chain A: R.48, K.236 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.48, A:R.48 Water bridges: A:R.48, A:K.236, A:K.236, A:K.236, A:K.236, A:K.236 Salt bridges: A:R.48, A:K.236

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.192, A.195, N.196, F.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.192, A:N.196, A:N.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthold, C.L. et al., Mechanism of Adp-Ribosylation Removal Revealed by the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-08-18

Peptides

ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE

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