SMTL ID : 5ue1.1

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in complex with adenine from Vibrio fischeri ES114

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

homo-dimer

Ligands

2 x 9DA: 9-DEAZAADENINE(Non-covalent)

9DA.1: 14 residues within 4Å: Chain A: S.79, A.80, G.81, V.154, F.155, V.156, V.175, E.176, M.177, S.200, D.201, A.203, F.211 Ligands: TRS.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.156, A:D.201, A:D.201 pi-Stacking: A:F.155 9DA.8: 14 residues within 4Å: Chain B: S.79, A.80, G.81, V.154, F.155, V.156, V.175, E.176, M.177, S.200, D.201, A.203, F.211 Ligands: TRS.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.156, B:D.201, B:D.201 pi-Stacking: B:F.155

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 11 residues within 4Å: Chain A: A.11, M.12, E.15, S.79, E.176, M.177, E.178, R.197, F.211 Ligands: 9DA.1, EDO.13 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.15, A:S.79, A:S.79, A:E.176, A:E.176, A:M.177, A:E.178, A:R.197, A:R.197 Water bridges: A:A.11 TRS.9: 10 residues within 4Å: Chain B: A.11, M.12, E.15, S.79, E.176, M.177, E.178, R.197, F.211 Ligands: 9DA.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.15, B:S.79, B:S.79, B:E.176, B:M.177, B:E.178, B:R.197, B:R.197 Water bridges: B:A.11

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: N.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.2, H2O.8 CA.4: 1 residues within 4Å: Chain A: D.21 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, H2O.7 CA.5: 3 residues within 4Å: Chain A: M.209, D.212, E.213 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.209, A:D.212, A:E.213, H2O.8, H2O.9

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: M.12, E.13, Q.14 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: V.145, R.146 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain A: M.115, Q.184 Chain B: I.53, G.54, K.55, V.56, A.57 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: M.12, E.13, Q.14 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: V.145, R.146 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 5 residues within 4Å: Chain A: F.211 Chain B: V.105, F.108, A.116 Ligands: TRS.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Vibrio fischeri ES114. To Be Published

Release Date

2017-01-18

Peptides

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase