SMTL ID : 3zbg.1

Crystal structure of wild-type SCP2 thiolase from Leishmania mexicana at 1.85 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

14 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: L.181, F.198, P.199, C.274, S.275, F.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.275 DMS.2: 5 residues within 4Å: Chain A: G.36, H.37, I.38, L.236, R.419 No protein-ligand interaction detected (PLIP) DMS.3: 2 residues within 4Å: Chain A: R.331, Y.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.331 pi-Cation interactions: A:Y.373 DMS.4: 4 residues within 4Å: Chain A: N.232, H.240, T.241, K.243 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.240 DMS.6: 3 residues within 4Å: Chain A: L.297, D.301, R.303 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.301 DMS.7: 1 residues within 4Å: Chain A: F.328 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.328 DMS.9: 6 residues within 4Å: Chain B: L.181, P.199, S.275, V.277, F.357 Ligands: MPD.17 No protein-ligand interaction detected (PLIP) DMS.10: 3 residues within 4Å: Chain B: A.435, N.456, I.457 No protein-ligand interaction detected (PLIP) DMS.11: 6 residues within 4Å: Chain A: Q.91, P.131, M.133 Chain B: I.147, N.151, C.312 No protein-ligand interaction detected (PLIP) DMS.12: 6 residues within 4Å: Chain A: I.147, C.312 Chain B: Q.91, P.131, A.132, M.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.151 DMS.13: 2 residues within 4Å: Chain A: Y.129 Chain B: F.328 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.322 pi-Cation interactions: B:F.328 DMS.14: 4 residues within 4Å: Chain B: M.217, N.250, K.258, R.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.270 DMS.16: 2 residues within 4Å: Chain B: R.331, Y.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.331, B:R.331 Water bridges: B:D.323 pi-Cation interactions: B:Y.373 DMS.18: 3 residues within 4Å: Chain B: M.271, C.274, Q.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.276 Water bridges: B:Y.228, B:C.274

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: F.196, P.199, F.259, M.271, C.274, V.277 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.196, A:P.199, A:F.259, A:V.277 MPD.8: 6 residues within 4Å: Chain B: M.206, A.210, F.215, T.216, M.217, Y.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.217 MPD.15: 7 residues within 4Å: Chain B: V.34, H.79, S.80, G.81, R.85, L.297, R.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.34 MPD.17: 8 residues within 4Å: Chain B: A.174, F.196, P.199, F.259, M.271, C.274, V.277 Ligands: DMS.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.196, B:P.199, B:F.259, B:F.259, B:V.277 Water bridges: B:S.275

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harijan, R.K. et al., Crystal Structures of Scp2-Thiolases of Trypanosomatidae, Human Pathogens Causing Widespread Tropical Diseases: The Importance for Catalysis of the Cysteine of the Unique Hdcf Loop. Biochem.J. (2013)

Release Date

2013-08-14

Peptides

3-KETOACYL-COA THIOLASE-LIKE PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-KETOACYL-COA THIOLASE-LIKE PROTEIN