SMTL ID : 5cce.1

Joint X-ray/neutron structure of wild type MTAN complexed with SRH and adenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x 2WP: S-ribosylhomocysteine(Non-covalent)

2WP.1: 20 residues within 4Å: Chain A: A.9, M.10, E.13, I.52, G.53, G.77, V.78, A.79, F.153, E.173, M.174, E.175, R.194, F.208, D.209 Chain B: L.104, F.107, H.109, P.115 Ligands: ADE.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.52, B:F.107 Hydrogen bonds: A:E.13, A:M.174, A:E.175, A:E.175, A:R.194, A:R.194 Salt bridges: A:R.194, B:H.109 Water bridges: B:H.109 2WP.4: 20 residues within 4Å: Chain A: L.104, F.107, H.109, P.115 Chain B: A.9, M.10, E.13, I.52, G.53, G.77, V.78, A.79, F.153, E.173, M.174, E.175, R.194, F.208, D.209 Ligands: ADE.5 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.52, A:F.107 Hydrogen bonds: B:E.13, B:M.174, B:E.175, B:E.175, B:R.194, B:R.194 Salt bridges: B:R.194, A:H.109 Water bridges: A:H.109

2 x ADE: ADENINE(Covalent)

ADE.2: 16 residues within 4Å: Chain A: V.78, A.79, G.80, Q.152, F.153, V.154, V.172, E.173, M.174, S.197, D.198, A.200, A.204, F.208 Ligands: 2WP.1, D8U.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.78, A:V.154, A:E.173, A:S.197, A:D.198, A:A.200 pi-Stacking: A:F.153 ADE.5: 16 residues within 4Å: Chain B: V.78, A.79, G.80, Q.152, F.153, V.154, V.172, E.173, M.174, S.197, D.198, A.200, A.204, F.208 Ligands: 2WP.4, D8U.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.78, B:G.80, B:V.154, B:E.173, B:S.197, B:D.198, B:A.200 pi-Stacking: B:F.153

2 x D8U: deuterium(1+)(Non-covalent)

D8U.3: 7 residues within 4Å: Chain A: A.79, G.80, S.197, D.198, A.200, F.208 Ligands: ADE.2 Protein-ligand interaction information (PLIP) not available D8U.6: 7 residues within 4Å: Chain B: A.79, G.80, S.197, D.198, A.200, F.208 Ligands: ADE.5 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banco, M.T. et al., Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-11-16

Peptides

5'-Methylthioadenosine Nucleosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'-Methylthioadenosine Nucleosidase

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