SMTL ID : 5jju.1

Crystal structure of Rv2837c complexed with 5'-pApA and 5'-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

1 x A- A: RNA (5'-R(P*AP*A)-3')(Non-covalent)

A-A.1: 21 residues within 4Å: Chain A: H.31, D.35, D.96, R.102, H.122, T.170, D.171, W.177, S.282, R.284, G.299, G.300, G.301, H.302, A.305, A.306, G.307, Y.308, T.309 Ligands: MN.2, MN.3 Protein-ligand interaction information (PLIP) not available

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

MN.2: 5 residues within 4Å: Chain A: D.37, D.96, H.121, D.171 Ligands: A-A.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:D.96, A:H.121, A:D.171, H2O.2 MN.3: 4 residues within 4Å: Chain A: H.31, D.35, D.96 Ligands: A-A.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, A:D.35, A:D.35, A:D.96, H2O.2 MN.4: 6 residues within 4Å: Chain B: D.37, D.96, H.121, T.141, D.171 Ligands: AMP.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.37, B:D.96, B:H.121, B:D.171, AMP.7 MN.5: 4 residues within 4Å: Chain B: H.31, D.35, D.96 Ligands: AMP.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.31, B:D.35, B:D.35, B:D.96, AMP.7

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 14 residues within 4Å: Chain B: R.102, H.122, E.253, S.282, R.284, G.299, G.300, G.301, A.305, A.306, G.307, Y.308, T.309 Ligands: AMP.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.102, B:R.102, B:E.253, B:S.282, B:G.307, B:T.309, B:T.309 Water bridges: B:K.272, B:K.272 Salt bridges: B:K.272, B:R.284 pi-Cation interactions: B:R.102 AMP.7: 13 residues within 4Å: Chain B: D.35, D.96, H.121, H.122, T.170, D.171, W.177, R.284, H.302, A.305 Ligands: MN.4, MN.5, AMP.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.96, B:T.170, B:R.284 Water bridges: B:L.304 Salt bridges: B:H.121, B:H.122, B:H.302 pi-Stacking: B:H.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Q. et al., Structural and biochemical insight into the mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP phosphodiesterase. J.Biol.Chem. (2016)

Release Date

2016-05-04

Peptides

Uncharacterized protein Rv2837c: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uncharacterized protein Rv2837c