SMTL ID : 1mqw.1

Structure of the MT-ADPRase in complex with three Mn2+ ions and AMPCPR, a Nudix enzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: A.76, E.97, E.142 Ligands: MN.2, ADV.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.76, A:E.97, H2O.1, H2O.1 MN.2: 7 residues within 4Å: Chain A: A.76, E.93, E.97, E.142 Ligands: MN.1, MN.3, ADV.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.93, A:E.97, A:E.142, H2O.1 MN.3: 4 residues within 4Å: Chain A: R.92, E.93 Ligands: MN.2, ADV.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.93, H2O.1, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain B: A.76, E.97, E.142 Ligands: MN.6, ADV.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.76, B:E.97, H2O.3, H2O.3 MN.6: 7 residues within 4Å: Chain B: A.76, E.93, E.97, E.142 Ligands: MN.5, MN.7, ADV.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.93, B:E.97, B:E.142, H2O.3 MN.7: 4 residues within 4Å: Chain B: R.92, E.93 Ligands: MN.6, ADV.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.93, H2O.3, H2O.3, H2O.3

2 x ADV: ALPHA-BETA METHYLENE ADP-RIBOSE(Non-covalent)

ADV.4: 19 residues within 4Å: Chain A: A.18, I.19, Q.62, R.64, A.76, G.77, L.78, E.93, E.97, H.139, H.140, E.141, E.142 Chain B: T.36, R.37, G.116 Ligands: MN.1, MN.2, MN.3 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.64, A:R.64, A:L.78, A:E.141, A:E.142, B:R.37, B:R.37, B:E.38 Water bridges: A:Q.62, A:H.139, A:E.141, A:E.142 pi-Cation interactions: B:R.37, B:R.37 ADV.8: 19 residues within 4Å: Chain A: T.36, R.37, G.116 Chain B: A.18, I.19, Q.62, R.64, A.76, G.77, L.78, E.93, E.97, H.139, H.140, E.141, E.142 Ligands: MN.5, MN.6, MN.7 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.64, B:R.64, B:L.78, B:E.141, B:E.142, A:R.37, A:R.37, A:E.38 Water bridges: B:Q.62, B:H.139, B:E.142 pi-Cation interactions: A:R.37, A:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, L.-W. et al., Structure and mechanism of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis. Structure (2003)

Release Date

2003-08-05

Peptides

ADPR pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ADPR pyrophosphatase

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