SMTL ID : 4xq2.1 (1 other biounit)

Ensemble refinement of cystathione gamma lyase (CalE6) D7G 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: 8 residues within 4Å: Chain A: Y.103, K.200, V.325, S.326, L.327, R.361 Chain B: Y.49, R.51 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.103, A:S.326, A:S.326, A:S.326 Water bridges: A:R.361 Salt bridges: A:R.361 MES.7: 11 residues within 4Å: Chain A: Y.49, R.51 Chain B: Y.103, N.150, K.200, V.325, S.326, L.327, T.341, R.361 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.103, B:N.150, B:S.326 Salt bridges: B:R.361 MES.16: 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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.326 Salt bridges: C:R.361 MES.21: 9 residues within 4Å: Chain C: Y.49, R.51 Chain D: Y.103, K.200, V.325, S.326, L.327, T.341, R.361 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.326 Salt bridges: D:R.361

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: L.89, R.171, D.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:R.171, A:D.219 GOL.3: 6 residues within 4Å: Chain A: R.19, P.20, S.21, P.30, H.32, E.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.19 Water bridges: A:A.22, A:T.24 GOL.4: 4 residues within 4Å: Chain A: E.68, L.187, A.188, R.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216 Water bridges: A:E.68, A:L.187, A:A.188 GOL.8: 8 residues within 4Å: Chain B: R.256, I.366, E.367, D.368, P.369 Chain C: G.10, S.251, L.252 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.366, B:D.368, C:G.10, C:S.251 GOL.9: 5 residues within 4Å: Chain B: E.68, R.69, L.187, A.188, R.216 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.187, B:R.216 GOL.10: 4 residues within 4Å: Chain A: A.104, G.105, G.108 Chain B: T.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.230 GOL.11: 5 residues within 4Å: Chain B: R.19, S.21, P.29, H.32, E.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.59 GOL.12: 6 residues within 4Å: Chain B: V.277, H.278, Y.279, E.284, H.285, P.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.278, B:Y.279, B:Y.279 Water bridges: B:H.285 GOL.13: 5 residues within 4Å: Chain B: H.166, G.169, A.170, R.171, D.192 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.192 GOL.14: 6 residues within 4Å: Chain A: R.51, T.230 Chain B: Y.103, A.104, G.105 Ligands: MES.7 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.51, A:R.51, A:T.230, B:Y.103 GOL.17: 5 residues within 4Å: Chain C: E.68, R.69, L.187, A.188, R.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.216, C:R.216 Water bridges: C:G.190 GOL.22: 5 residues within 4Å: Chain D: E.68, R.69, A.70, L.187, A.188 No protein-ligand interaction detected (PLIP) GOL.23: 2 residues within 4Å: Chain D: T.229, T.230 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.230 GOL.24: 5 residues within 4Å: Chain D: L.89, R.171, D.219, L.220, A.223 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.171

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

CL.5: 3 residues within 4Å: Chain A: R.171, D.192, D.217 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: M.340 Chain B: R.39, F.48 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: M.295 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: R.171, D.192 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: R.115 Chain D: R.91 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain D: R.171 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain D: M.295, S.296 Ligand excluded by PLIP

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

FMT.18: 5 residues within 4Å: Chain C: L.89, R.171, D.219, L.220, A.223 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.171, C:R.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yennamalli, R.M. et al., The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora. To Be Published

Release Date

2015-04-15

Peptides

CalE6: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CalE6

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