SMTL ID : 2yvp.1

Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: A.74, E.90, E.94, E.139 Ligands: MG.2, MG.3, RBY.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.90, A:E.94, A:E.139, H2O.3, H2O.17 MG.2: 6 residues within 4Å: Chain A: A.74, E.90, E.94, E.139 Ligands: MG.1, RBY.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.74, A:E.94, H2O.4, H2O.7 MG.3: 5 residues within 4Å: Chain A: R.89, E.90, E.136 Ligands: MG.1, RBY.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.90, H2O.17, H2O.49, H2O.54, H2O.60 MG.5: 7 residues within 4Å: Chain B: A.74, E.90, E.94, E.139 Ligands: MG.6, MG.7, RBY.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.90, B:E.94, B:E.139, H2O.136, H2O.150 MG.6: 6 residues within 4Å: Chain B: A.74, E.90, E.94, E.139 Ligands: MG.5, RBY.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.74, B:E.94, H2O.137, H2O.140 MG.7: 5 residues within 4Å: Chain B: R.89, E.90, E.136 Ligands: MG.5, RBY.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.90, H2O.150, H2O.182, H2O.187, H2O.193

2 x RBY: METHYLENE ADP-BETA-XYLOSE(Non-covalent)

RBY.4: 25 residues within 4Å: Chain A: P.16, V.17, A.43, R.62, A.74, G.75, K.76, E.90, E.94, V.117, F.119, E.136, E.137, G.138, E.139 Chain B: L.32, T.33, Y.34, V.35, Q.111, S.113, F.114 Ligands: MG.1, MG.2, MG.3 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.62, A:R.62, A:K.76, A:G.138, B:V.35, B:V.35, B:Q.111, B:S.113 Water bridges: A:Q.60, A:Q.60, A:A.74, A:A.74, A:R.89, A:E.136, B:S.113 pi-Stacking: B:Y.34 RBY.8: 25 residues within 4Å: Chain A: L.32, T.33, Y.34, V.35, Q.111, S.113, F.114 Chain B: P.16, V.17, A.43, R.62, A.74, G.75, K.76, E.90, E.94, V.117, F.119, E.136, E.137, G.138, E.139 Ligands: MG.5, MG.6, MG.7 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.62, B:R.62, B:K.76, B:G.138, A:V.35, A:V.35, A:Q.111, A:S.113 Water bridges: B:Q.60, B:Q.60, B:A.74, B:A.74, B:R.89, A:S.113 pi-Stacking: A:Y.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wakamatsu, T. et al., Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8. J.Bacteriol. (2008)

Release Date

2008-02-26

Peptides

MutT/nudix family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MutT/nudix family protein

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