SMTL ID : 4glj.1

Crystal structure of methylthioadenosine phosphorylase in complex with rhodamine B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

6 x RHB: N-[9-(2-carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene]-N-ethylethanaminium(Non-covalent)

RHB.1: 18 residues within 4Å: Chain A: S.22, Y.25, H.65, H.69, P.73, A.98, F.179, M.198, I.239, L.242, M.243 Chain C: H.136, Q.275, L.277, V.278 Ligands: RHB.2, PO4.3, CL.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.25, A:P.73, A:A.98, A:F.179, A:F.179, A:I.239, C:V.278 RHB.2: 17 residues within 4Å: Chain A: A.98, V.99, G.100, F.179, I.196, G.197, M.198, T.221, D.222, F.223, D.224, C.225, N.229, A.238, L.242 Ligands: RHB.1, CL.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.179, A:I.196, A:N.229, A:A.238, A:L.242 Hydrogen bonds: A:D.222 Water bridges: A:T.221, A:F.223 pi-Stacking: A:F.179, A:F.179, A:F.179 RHB.6: 18 residues within 4Å: Chain A: H.136, Q.275, L.277, V.278 Chain B: S.22, Y.25, H.65, H.69, P.73, A.98, F.179, M.198, I.239, L.242, M.243 Ligands: RHB.7, PO4.8, CL.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.25, B:P.73, B:A.98, B:F.179, B:F.179, B:I.239, A:V.278 RHB.7: 17 residues within 4Å: Chain B: A.98, V.99, G.100, F.179, I.196, G.197, M.198, T.221, D.222, F.223, D.224, C.225, N.229, A.238, L.242 Ligands: RHB.6, CL.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.179, B:I.196, B:N.229, B:A.238, B:L.242 Hydrogen bonds: B:D.222 Water bridges: B:T.221, B:F.223 pi-Stacking: B:F.179, B:F.179, B:F.179 RHB.11: 18 residues within 4Å: Chain B: H.136, Q.275, L.277, V.278 Chain C: S.22, Y.25, H.65, H.69, P.73, A.98, F.179, M.198, I.239, L.242, M.243 Ligands: RHB.12, PO4.13, CL.15 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.25, C:P.73, C:A.98, C:F.179, C:F.179, C:I.239, B:V.278 RHB.12: 17 residues within 4Å: Chain C: A.98, V.99, G.100, F.179, I.196, G.197, M.198, T.221, D.222, F.223, D.224, C.225, N.229, A.238, L.242 Ligands: RHB.11, CL.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.179, C:I.196, C:N.229, C:A.238, C:L.242 Hydrogen bonds: C:D.222 Water bridges: C:T.221, C:F.223 pi-Stacking: C:F.179, C:F.179, C:F.179

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: G.21, S.22, R.64, H.65, S.97, A.98, T.199 Ligands: RHB.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.22, A:A.98, A:A.98 Water bridges: A:M.198, A:M.198 Salt bridges: A:R.64, A:H.65 PO4.8: 8 residues within 4Å: Chain B: G.21, S.22, R.64, H.65, S.97, A.98, T.199 Ligands: RHB.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.22, B:A.98, B:A.98 Water bridges: B:M.198, B:M.198 Salt bridges: B:R.64, B:H.65 PO4.13: 8 residues within 4Å: Chain C: G.21, S.22, R.64, H.65, S.97, A.98, T.199 Ligands: RHB.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.22, C:A.98, C:A.98 Water bridges: C:M.198, C:M.198 Salt bridges: C:R.64, C:H.65

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

CL.4: 4 residues within 4Å: Chain A: D.222, N.229, S.234 Ligands: RHB.2 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Ligands: RHB.1 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: D.222, N.229, S.234 Ligands: RHB.7 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Ligands: RHB.6 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: D.222, N.229, S.234 Ligands: RHB.12 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Ligands: RHB.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bartasun, P. et al., A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an antarctic soil metagenomic library. Plos One (2013)

Release Date

2013-02-20

Peptides

RsfP: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

RsfP

Related Entries With Identical Sequence