SMTL ID : 4q31.2 (1 other biounit)

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 10 residues within 4Å: Chain A: Y.103, K.200, V.325, S.326, L.327, T.341, R.361 Chain B: Y.49, R.51 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.326 Salt bridges: A:R.361 MES.7: 9 residues within 4Å: Chain A: Y.49 Chain B: Y.103, K.200, V.325, S.326, L.327, T.341, R.361 Ligands: GOL.4 No protein-ligand interaction detected (PLIP) MES.13: 9 residues within 4Å: Chain C: Y.103, K.200, V.325, S.326, L.327, T.341, R.361 Chain D: Y.49, R.51 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.103, C:S.326 Water bridges: C:R.361, D:R.51, D:R.51 Salt bridges: C:R.361 MES.21: 8 residues within 4Å: Chain C: Y.49 Chain D: Y.103, K.200, V.325, S.326, L.327, R.361 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.103, D:S.326 Water bridges: D:N.150 Salt bridges: D:R.361

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

CL.2: 3 residues within 4Å: Chain A: R.171, D.192, D.217 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: R.171 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: R.171, D.217 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: R.171, D.217 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: R.39 Chain D: V.325, M.340 Ligand excluded by PLIP

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.68, R.69, L.187, A.188, R.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.187, A:R.216 Water bridges: A:E.68, A:A.188, A:G.190 GOL.4: 6 residues within 4Å: Chain A: R.51, T.230 Chain B: Y.103, A.104, G.105 Ligands: MES.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.51, A:R.51, A:T.230, B:Y.103, B:Y.103 GOL.5: 5 residues within 4Å: Chain A: L.89, R.171, D.219, L.220, A.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.171, A:R.171 GOL.6: 6 residues within 4Å: Chain A: Y.103, A.104, G.105 Chain B: R.51, T.230 Ligands: MES.1 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.51, B:R.51, B:T.230, A:Y.103, A:Y.103 GOL.9: 5 residues within 4Å: Chain B: L.89, R.171, D.219, L.220, A.223 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.171, B:R.171, B:D.217 Water bridges: B:L.220, B:A.223 GOL.10: 3 residues within 4Å: Chain B: R.256 Chain C: L.252, H.255 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Water bridges: C:S.251, C:R.256, B:L.252, B:R.256 Hydrogen bonds: B:R.256, B:R.256 GOL.11: 5 residues within 4Å: Chain B: E.68, R.69, L.187, A.188, R.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.216, B:R.216 Water bridges: B:A.188 GOL.15: 6 residues within 4Å: Chain C: E.68, R.69, P.71, L.187, A.188, R.216 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.68, C:R.216, C:R.216 Water bridges: C:A.188 GOL.16: 4 residues within 4Å: Chain B: S.251, L.252, H.255 Chain C: R.256 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.256, B:S.251 Water bridges: C:R.256, B:R.256 GOL.17: 7 residues within 4Å: Chain C: R.51, T.230 Chain D: Y.103, A.104, G.105, G.108 Ligands: MES.21 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.51, C:R.51, C:T.230, D:Y.103 Water bridges: C:T.230 GOL.18: 5 residues within 4Å: Chain C: R.39, R.40 Chain D: L.315, C.323, L.339 No protein-ligand interaction detected (PLIP) GOL.19: 4 residues within 4Å: Chain C: A.293, Q.294, M.295, S.296 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.294 GOL.24: 5 residues within 4Å: Chain D: E.68, R.69, L.187, A.188, R.216 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.187, D:R.216 Water bridges: D:E.68, D:A.188

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.12: 5 residues within 4Å: Chain B: E.62, P.71, F.72, A.73, R.225 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.73, B:A.73, B:R.225 Water bridges: B:R.225 FMT.20: 3 residues within 4Å: Chain C: L.89, R.171, A.223 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.171, C:R.171 FMT.25: 2 residues within 4Å: Chain D: L.89, R.171 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.171, D:R.171 Water bridges: D:L.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. Struct Dyn (2016)

Release Date

2014-05-07

Peptides

cystathione gamma lyase CalE6: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

cystathione gamma lyase CalE6

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