SMTL ID : 9ubg.1

Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 10 residues within 4Å: Chain A: K.117, Y.198, Q.201, H.208, Q.232, H.235, E.275, L.277, E.288, N.290 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.208, A:Q.232, A:E.275, A:N.290 Salt bridges: A:K.117 ADP.4: 12 residues within 4Å: Chain B: K.117, F.156, Y.198, Q.201, H.208, Q.232, H.235, E.275, L.277, I.287, E.288, N.290 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.198, B:Y.198, B:Q.201, B:Q.232, B:E.275, B:E.288, B:N.290 Salt bridges: B:K.117, B:K.237 ADP.8: 10 residues within 4Å: Chain C: Y.198, Q.201, H.208, Q.232, H.235, E.275, L.277, I.287, E.288, N.290 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.208, C:Q.232, C:E.275, C:E.288, C:E.288 ADP.11: 9 residues within 4Å: Chain D: Q.201, A.202, H.208, Q.232, H.235, E.275, L.277, E.288, N.290 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.173, D:Q.201, D:H.208, D:Q.232, D:N.290, D:N.290 Salt bridges: D:K.117

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.533, K.703, H.732, H.734, Q.768 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.533, A:H.732, A:H.734 ZN.5: 5 residues within 4Å: Chain B: D.533, K.703, H.732, H.734, Q.768 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.533, B:H.732, B:H.734 ZN.9: 5 residues within 4Å: Chain C: D.533, K.703, H.732, H.734, Q.768 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.533, C:H.732, C:H.734 ZN.12: 5 residues within 4Å: Chain D: D.533, K.703, H.732, H.734, Q.768 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.533, D:H.732, D:H.734

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

ACO.3: 19 residues within 4Å: Chain A: R.362, E.412, R.414, R.416, S.456, A.457, D.458, R.459, E.1007, N.1031, R.1035 Chain D: R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:E.412 Hydrogen bonds: A:R.414, A:R.414, A:R.416, A:D.458, A:R.459, A:N.1031, D:R.42 Salt bridges: A:R.362, A:R.416, A:R.459, A:R.1035 ACO.6: 21 residues within 4Å: Chain B: R.362, A.411, E.412, R.414, R.416, A.455, S.456, A.457, D.458, R.459, E.1007, N.1031, R.1035 Chain C: R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:E.412 Hydrogen bonds: B:R.414, B:R.416, B:A.457, B:D.458, B:R.459, B:N.1031, C:R.42 Salt bridges: B:R.362, B:R.416, B:R.459, B:R.1035 ACO.7: 20 residues within 4Å: Chain B: R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47 Chain C: R.362, A.411, E.412, R.414, R.416, S.456, A.457, D.458, R.459, E.1007, N.1031, R.1035 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:E.412 Hydrogen bonds: C:R.414, C:R.416, C:A.457, C:D.458, C:R.459, C:N.1031, B:R.42 Salt bridges: C:R.362, C:R.416, C:R.459, C:R.1035 ACO.10: 21 residues within 4Å: Chain A: F.18, Y.22, R.42, L.43, K.44, A.45, D.46, E.47, S.48 Chain D: R.362, E.412, R.414, R.416, S.456, A.457, D.458, R.459, G.1005, E.1007, N.1031, R.1035 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.362, D:R.414, D:R.416, D:A.457, D:D.458, D:R.459, D:N.1031, A:S.48 Salt bridges: D:R.362, D:R.416, D:R.459, D:R.1035 Hydrophobic interactions: A:Y.22

Links

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Citation

Singh, A. et al., Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis in complex with Acetyl-CoA and ADP. To Be Published

Release Date

2025-05-07

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase