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 2.70 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: F.156, K.158, G.163, G.164, G.165, E.200, Q.201, A.202, V.203, H.208, Q.232, H.235, K.237, E.275, L.277, I.287, E.288, T.441 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.158, A:G.164, A:G.165, A:Q.201, A:Q.232, A:Q.232, A:Q.232 pi-Stacking: A:F.156, A:F.156 pi-Cation interactions: A:K.158 ADP.4: 19 residues within 4Å: Chain B: F.156, K.158, G.163, G.164, G.165, M.168, E.200, Q.201, A.202, V.203, H.208, Q.232, H.235, K.237, E.275, L.277, I.287, E.288, T.441 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.158, B:G.164, B:G.165, B:E.200, B:Q.201, B:Q.232, B:Q.232, B:E.288 pi-Stacking: B:F.156, B:F.156 pi-Cation interactions: B:K.158 ADP.8: 18 residues within 4Å: Chain C: F.156, K.158, G.163, G.164, G.165, M.168, E.200, Q.201, A.202, V.203, H.208, Q.232, H.235, E.275, L.277, I.287, E.288, N.290 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.158, C:G.164, C:Q.201, C:Q.232, C:H.235 pi-Stacking: C:F.156 pi-Cation interactions: C:K.158 ADP.11: 19 residues within 4Å: Chain D: F.156, K.158, G.163, G.164, G.165, M.168, E.200, Q.201, A.202, V.203, H.208, Q.232, H.235, E.275, L.277, I.287, E.288, N.290, T.441 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.158, D:G.164, D:G.165, D:E.200, D:Q.201, D:V.203, D:Q.232, D:Q.232, D:E.275, D:E.288, D:N.290 pi-Stacking: D:F.156 pi-Cation interactions: D:K.158

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: 22 residues within 4Å: Chain A: R.362, R.408, A.411, R.414, R.416, S.456, A.457, R.459, G.1005, E.1007, L.1008, N.1031, R.1035 Chain D: F.18, R.19, Y.22, R.42, L.43, K.44, A.45, D.46, S.48 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:R.408, D:Y.22 Hydrogen bonds: A:R.362, A:R.414, A:R.416, A:S.456, A:R.459, A:N.1031, D:S.48, D:S.48 Salt bridges: A:R.362, A:R.416, A:R.459, A:R.1035 ACO.6: 30 residues within 4Å: Chain B: R.362, R.408, A.411, E.412, R.414, R.416, S.456, A.457, D.458, R.459, G.460, T.461, L.1002, G.1005, V.1006, E.1007, L.1008, L.1030, N.1031, R.1035 Chain C: F.18, R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47, S.48 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:Y.22, B:R.408 Hydrogen bonds: C:S.48, C:S.48, B:R.362, B:R.414, B:R.414, B:R.414, B:R.416, B:S.456, B:R.459, B:N.1031 Salt bridges: B:R.362, B:R.416, B:R.459, B:R.1035 ACO.7: 30 residues within 4Å: Chain B: F.18, R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47, S.48 Chain C: R.362, R.408, A.411, E.412, R.414, R.416, S.456, A.457, D.458, R.459, G.460, T.461, L.1002, G.1005, V.1006, E.1007, L.1008, L.1030, N.1031, R.1035 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain C Hydrophobic interactions: B:Y.22, C:R.408 Hydrogen bonds: B:A.45, B:S.48, C:R.362, C:R.414, C:R.414, C:R.416, C:S.456, C:R.459, C:N.1031 Salt bridges: C:R.362, C:R.416, C:R.459, C:R.1035 ACO.10: 30 residues within 4Å: Chain A: F.18, R.19, Y.22, R.42, L.43, K.44, A.45, D.46, E.47, S.48 Chain D: R.362, R.408, A.411, E.412, R.414, R.416, S.456, A.457, D.458, R.459, G.460, T.461, L.1002, G.1005, V.1006, E.1007, L.1008, L.1030, N.1031, R.1035 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:R.408, A:Y.22 Hydrogen bonds: D:R.362, D:R.414, D:R.414, D:R.416, D:S.456, D:R.459, D:N.1031, A:A.45, A:S.48 Salt bridges: D:R.362, D:R.416, D:R.459, D:R.1035

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
C

C
D

D
B

Pyruvate carboxylase