SMTL ID : 6ee1.1

Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-tetramer

Ligands

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 24 residues within 4Å: Chain A: V.693, R.694, D.695, Q.696, N.697, T.698, R.704, Q.705, K.706, R.707, M.709, T.710, V.728, T.729, P.730, T.731, D.733, N.734, Y.736, Q.737, K.740, H.744, K.784 Chain C: R.685 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.693, A:D.733 Hydrogen bonds: A:Q.696, A:T.698, A:T.698, A:R.704, A:Q.705, A:Q.705, A:Q.705, A:K.706, A:R.707, A:L.708, A:M.709, A:T.710, A:D.733, A:D.733, A:D.733, A:N.734 Water bridges: A:L.703 Salt bridges: A:R.707, A:K.740, A:H.744, A:K.784 ACO.3: 24 residues within 4Å: Chain B: V.693, R.694, D.695, Q.696, N.697, T.698, R.704, Q.705, K.706, R.707, L.708, M.709, T.710, V.728, T.729, P.730, T.731, D.733, N.734, Y.736, Q.737, K.740, H.744, K.784 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.693, B:D.733 Hydrogen bonds: B:Q.696, B:T.698, B:T.698, B:R.704, B:Q.705, B:Q.705, B:K.706, B:R.707, B:M.709, B:T.710, B:T.710, B:T.710, B:T.731, B:D.733, B:D.733, B:D.733 Water bridges: B:L.703, B:Q.705, B:L.708 Salt bridges: B:R.707, B:H.744, B:K.784 ACO.5: 25 residues within 4Å: Chain A: R.685 Chain C: V.693, R.694, D.695, Q.696, N.697, T.698, R.704, Q.705, K.706, R.707, L.708, M.709, T.710, Y.727, V.728, T.729, P.730, T.731, D.733, N.734, Y.736, Q.737, K.740, H.744 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Y.727, C:D.733 Hydrogen bonds: C:Q.696, C:Q.696, C:T.698, C:T.698, C:R.704, C:Q.705, C:Q.705, C:K.706, C:R.707, C:L.708, C:M.709, C:T.710, C:T.710, C:D.733, C:D.733, C:D.733, C:N.734 Water bridges: C:R.704 Salt bridges: C:R.707, C:K.740, C:H.744 ACO.7: 25 residues within 4Å: Chain B: R.685 Chain D: V.693, R.694, D.695, Q.696, N.697, T.698, R.704, Q.705, K.706, R.707, L.708, M.709, T.710, V.728, T.729, P.730, T.731, D.733, N.734, Y.736, Q.737, K.740, H.744, K.784 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:V.693, D:D.733 Hydrogen bonds: D:Q.696, D:T.698, D:T.698, D:Q.705, D:K.706, D:R.707, D:L.708, D:M.709, D:T.710, D:T.710, D:T.710, D:T.731, D:D.733, D:D.733, D:D.733 Water bridges: D:L.703, D:R.704 Salt bridges: D:R.707, D:K.740, D:H.744, D:K.784

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: I.57, A.470, A.473, Q.502 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.470, A:A.473, H2O.5, H2O.6 MG.4: 4 residues within 4Å: Chain B: I.57, A.470, A.473, Q.502 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.470, B:A.473, H2O.10, H2O.11 MG.6: 3 residues within 4Å: Chain C: A.470, A.473, Q.502 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.470, C:A.473, H2O.16, H2O.16 MG.8: 4 residues within 4Å: Chain D: I.57, A.470, A.473, Q.502 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.470, D:A.473, H2O.21, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhusal, R.P. et al., Acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2. Nat Commun (2019)

Release Date

2019-08-14

Peptides

Isocitrate lyase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isocitrate lyase 2

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