SMTL ID : 7cmy.1

Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.104, D.148, K.184 Ligands: SIN.2, GLV.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.148 MG.4: 7 residues within 4Å: Chain B: W.89, D.104, D.148, E.150, K.184 Ligands: SIN.5, GLV.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.148 MG.7: 5 residues within 4Å: Chain C: D.104, D.148, K.184 Ligands: SIN.8, GLV.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.148 MG.10: 7 residues within 4Å: Chain D: W.89, D.104, D.148, E.150, K.184 Ligands: SIN.11, GLV.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.148

4 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 13 residues within 4Å: Chain A: D.104, K.184, C.186, G.187, H.188, R.223, E.280, N.308, S.310, S.312, T.342 Ligands: MG.1, GLV.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.342 Hydrogen bonds: A:D.104, A:G.187, A:N.308, A:S.310, A:S.312 Salt bridges: A:K.184, A:H.188, A:R.223 SIN.5: 12 residues within 4Å: Chain B: D.104, C.186, G.187, H.188, R.223, E.280, N.308, S.310, S.312, T.342 Ligands: MG.4, GLV.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.342 Hydrogen bonds: B:G.187, B:N.308, B:N.308, B:S.310, B:S.312 Salt bridges: B:K.184, B:H.188, B:R.223 SIN.8: 13 residues within 4Å: Chain C: D.104, K.184, C.186, G.187, H.188, R.223, E.280, N.308, S.310, S.312, T.342 Ligands: MG.7, GLV.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.342 Hydrogen bonds: C:D.104, C:G.187, C:N.308, C:S.310, C:S.312, C:T.342 Salt bridges: C:K.184, C:H.188, C:R.223 SIN.11: 12 residues within 4Å: Chain D: D.104, C.186, G.187, H.188, R.223, E.280, N.308, S.310, S.312, T.342 Ligands: MG.10, GLV.12 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:T.342 Hydrogen bonds: D:G.187, D:E.280, D:N.308, D:N.308, D:S.310, D:S.312, D:T.342 Salt bridges: D:K.184, D:H.188, D:R.223

4 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.3: 11 residues within 4Å: Chain A: Y.85, S.87, G.88, W.89, D.104, D.148, H.175, R.223, T.342 Ligands: MG.1, SIN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.88, A:W.89, A:R.223 GLV.6: 12 residues within 4Å: Chain B: Y.85, S.87, G.88, W.89, D.104, D.148, H.175, R.223, W.278, T.342 Ligands: MG.4, SIN.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.85, B:G.88, B:W.89, B:R.223 GLV.9: 11 residues within 4Å: Chain C: Y.85, S.87, G.88, W.89, D.104, D.148, H.175, R.223, T.342 Ligands: MG.7, SIN.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.85, C:G.88, C:W.89, C:R.223 GLV.12: 12 residues within 4Å: Chain D: Y.85, S.87, G.88, W.89, D.104, D.148, H.175, R.223, W.278, T.342 Ligands: MG.10, SIN.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.88, D:W.89, D:R.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, K. et al., Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate. To Be Published

Release Date

2021-08-04

Peptides

Isocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
C

D
A

Isocitrate lyase

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