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

Structural and functional insights of DR2231 protein, the MazG-like nucleoside triphosphate pyrophosphohydrolase from Deinococcus radiodurans, complex with Gd

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.25 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.25 Salt bridges: A:R.25 SO4.2: 2 residues within 4Å: Chain A: R.124, K.128 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.124, A:K.128 SO4.3: 8 residues within 4Å: Chain A: A.138, D.139, V.140, R.141 Chain B: A.80, P.81, H.84 Ligands: GOL.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.140, A:R.141 Water bridges: A:A.138, B:H.84 Salt bridges: B:H.84 SO4.9: 3 residues within 4Å: Chain A: L.65, A.69 Chain B: R.44 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.44 SO4.10: 5 residues within 4Å: Chain A: Q.148 Chain B: S.75, A.76, G.77, D.78 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:E.145 Hydrogen bonds: B:S.75, B:S.75, B:A.76, B:G.77

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: E.33 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain A: E.53, H.84, D.88, Y.91, V.92 Chain B: V.111, N.115 Ligands: GD.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.53, A:D.88, B:N.115, B:N.115 GOL.6: 4 residues within 4Å: Chain A: R.141 Chain B: A.80, P.81 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.141, A:R.141 GOL.7: 4 residues within 4Å: Chain A: S.75, A.76, G.77 Chain B: Q.148 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.75, A:G.77, B:Q.148, B:Q.148 Water bridges: A:A.76 GOL.11: 5 residues within 4Å: Chain B: A.29, T.31, L.42, L.45, Q.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.99, B:Q.99, B:Q.99 GOL.12: 8 residues within 4Å: Chain A: A.80, P.81, H.84 Chain B: A.138, D.139, V.140, R.141, G.142 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.138, B:D.139, B:D.139, B:V.140, B:R.141, B:R.141, A:A.80 GOL.13: 2 residues within 4Å: Chain B: R.124, K.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.124, B:R.124, B:K.128 GOL.14: 4 residues within 4Å: Chain B: P.32, E.33, R.34, T.36 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.33, B:R.34, B:T.36 GOL.15: 3 residues within 4Å: Chain B: K.118, K.128, K.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.118, B:K.128, B:K.131

2 x GD: GADOLINIUM ATOM(Non-covalent)

GD.8: 5 residues within 4Å: Chain A: E.53, E.56, E.85, D.88 Ligands: GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.53, A:E.56, A:E.85, A:D.88, H2O.4 GD.16: 4 residues within 4Å: Chain B: E.53, E.56, E.85, D.88 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.53, B:E.56, B:D.88, H2O.8, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, A.M.D. et al., Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans. J.Biol.Chem. (2011)

Release Date

2011-07-06

Peptides

DR2231: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DR2231

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