SMTL ID : 8hcr.1

Cryo-EM structure of the Mycobacterium tuberculosis cytochrome bcc:aa3 supercomplex and a novel inhibitor targeting subunit cytochrome cI

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-mer

Ligands

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: C.353, H.355, L.356, G.357, C.358, C.372, H.375, S.377 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.353, A:H.355, A:C.372, A:H.375 FES.8: 8 residues within 4Å: Chain J: C.353, H.355, L.356, G.357, C.358, C.372, H.375, S.377 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.353, J:H.355, J:C.372, J:H.375

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 21 residues within 4Å: Chain B: F.45, G.48, E.49, A.51, L.52, F.121, I.125, H.128, L.129, R.131, I.132, A.137, R.142, N.145, W.146, G.149, I.228, H.231, V.235, H.240, T.241 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:A.51, B:F.121, B:I.125, B:I.132, B:N.145, B:W.146, B:I.228, B:V.235 Hydrogen bonds: B:G.48, B:T.241 Salt bridges: B:H.128, B:R.131, B:R.142, B:H.240, B:H.240 pi-Stacking: B:H.128 pi-Cation interactions: B:H.231 Metal complexes: B:H.128, B:H.231 HEM.3: 16 residues within 4Å: Chain B: L.58, L.59, G.62, V.63, L.65, T.66, R.111, H.114, H.115, E.159, G.160, G.163, Y.164, H.216, I.217 Chain K: L.218 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain K, Hydrophobic interactions: B:L.58, B:L.59, B:L.65, B:L.65, B:H.115, B:E.159, B:I.217, K:L.218 Hydrogen bonds: B:R.111 Salt bridges: B:R.111, B:R.111, B:H.115 pi-Stacking: B:H.114 Metal complexes: B:H.114, B:H.216 HEM.9: 21 residues within 4Å: Chain K: F.45, G.48, E.49, A.51, L.52, F.121, I.125, H.128, L.129, R.131, I.132, A.137, R.142, N.145, W.146, G.149, I.228, H.231, V.235, H.240, T.241 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:A.51, K:F.121, K:I.125, K:I.132, K:N.145, K:W.146, K:I.228 Hydrogen bonds: K:L.47, K:G.48, K:T.241 Salt bridges: K:H.128, K:R.131, K:R.142, K:H.240, K:H.240 pi-Stacking: K:H.128 Metal complexes: K:H.128, K:H.231 HEM.10: 18 residues within 4Å: Chain B: L.218 Chain K: L.58, L.59, G.62, V.63, F.69, R.111, H.114, H.115, A.118, E.159, G.160, G.163, Y.164, P.167, H.216, I.217, N.287 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain K, Hydrophobic interactions: B:L.218, K:L.58, K:L.59, K:F.69, K:A.118 Hydrogen bonds: K:N.287 Salt bridges: K:R.111, K:R.111 Metal complexes: K:H.114

4 x HEC: HEME C(Non-covalent)(Covalent)

HEC.4: 15 residues within 4Å: Chain C: S.72, C.73, C.76, H.77, H.87, P.89, L.91, V.94, A.98, V.99, Q.102, M.108, P.109, Q.213 Chain M: W.160 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain M, Hydrophobic interactions: C:C.76, C:A.98, C:V.99, C:Q.102, C:P.109, C:P.109, M:W.160 Hydrogen bonds: C:Q.213 pi-Cation interactions: C:H.77 HEC.5: 17 residues within 4Å: Chain A: Y.363 Chain C: F.101, R.107, N.173, C.174, S.176, C.177, H.178, L.187, Y.192, P.194, I.204, Q.213, N.214, M.215, P.216, F.218 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:L.187, C:P.194, C:I.204, C:Q.213, C:N.214, C:M.215, C:F.218 Hydrogen bonds: C:Q.213 Salt bridges: C:R.107, C:R.107 Metal complexes: C:H.178 HEC.11: 14 residues within 4Å: Chain D: W.160 Chain L: S.72, C.73, C.76, H.77, H.87, P.89, L.91, V.94, A.98, V.99, Q.102, P.109, Q.213 10 PLIP interactions: 10 interactions with chain L, Hydrophobic interactions: L:C.73, L:C.76, L:P.89, L:L.91, L:V.99, L:Q.102, L:P.109 Hydrogen bonds: L:Q.213 pi-Stacking: L:H.77 Metal complexes: L:H.77 HEC.12: 21 residues within 4Å: Chain J: Y.363 Chain L: R.107, N.173, C.174, S.176, C.177, H.178, L.187, Y.192, P.194, D.195, L.196, A.199, I.204, A.207, M.208, P.212, Q.213, N.214, M.215, P.216 11 PLIP interactions: 11 interactions with chain L, Hydrophobic interactions: L:N.173, L:L.187, L:P.194, L:L.196, L:I.204, L:A.207, L:M.208, L:N.214, L:P.216 Hydrogen bonds: L:R.107 Metal complexes: L:H.178

4 x HEA: HEME-A(Non-covalent)(Covalent)

HEA.6: 19 residues within 4Å: Chain E: W.151, W.260, V.267, H.313, H.314, T.337, G.338, F.341, G.373, G.376, V.377, L.379, T.389, V.394, H.397, F.398, V.401, L.402, R.459 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:W.151, E:W.260, E:V.267, E:T.337, E:F.341, E:F.341, E:V.377, E:L.379, E:V.394, E:F.398, E:V.401, E:V.401, E:L.402 Salt bridges: E:R.459 pi-Stacking: E:H.313 pi-Cation interactions: E:H.264, E:H.397 Metal complexes: E:H.397 HEA.7: 19 residues within 4Å: Chain E: F.52, G.56, L.57, R.63, F.83, H.86, M.90, W.151, F.398, H.399, L.402, F.403, F.446, R.459, R.460, A.481, L.484, G.485, F.489 16 PLIP interactions: 16 interactions with chain E, Hydrophobic interactions: E:F.52, E:F.52, E:L.57, E:M.90, E:F.398, E:L.402, E:F.446, E:A.481, E:F.489 Hydrogen bonds: E:W.151, E:R.460 Salt bridges: E:R.459, E:R.459, E:R.460 pi-Cation interactions: E:H.399 Metal complexes: E:H.399 HEA.13: 21 residues within 4Å: Chain N: W.151, W.260, V.267, H.313, H.314, A.334, T.337, G.338, G.373, G.376, V.377, L.379, A.380, D.385, T.389, H.397, F.398, V.401, L.402, R.459, R.460 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:W.151, N:W.260, N:V.267, N:T.337, N:V.377, N:V.377, N:L.379, N:F.398, N:V.401, N:V.401, N:L.402 Hydrogen bonds: N:W.151, N:H.314 Salt bridges: N:R.459, N:R.460 pi-Cation interactions: N:H.264, N:H.313 Metal complexes: N:H.397 HEA.14: 21 residues within 4Å: Chain N: F.52, G.56, L.57, A.59, R.63, F.79, F.83, H.86, M.90, W.151, F.398, H.399, L.402, F.403, F.446, R.459, R.460, A.481, L.484, G.485, F.489 19 PLIP interactions: 19 interactions with chain N, Hydrophobic interactions: N:F.52, N:F.52, N:L.57, N:M.90, N:F.398, N:F.398, N:L.402, N:F.403, N:F.446, N:A.481, N:F.489 Hydrogen bonds: N:R.460 Salt bridges: N:R.459, N:R.460 pi-Stacking: N:H.86, N:H.399, N:H.399 Metal complexes: N:H.86, N:H.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathiyazakan, V. et al., Cryo-Electron Microscopy Structure of the Mycobacterium tuberculosi s Cytochrome bcc : aa 3 Supercomplex and a Novel Inhibitor Targeting Subunit Cytochrome c I. Antimicrob.Agents Chemother. (2023)

Release Date

2023-05-03

Peptides

Cytochrome bc1 complex Rieske iron-sulfur subunit: AJ
Cytochrome bc1 complex cytochrome b subunit: BK
Cytochrome bc1 complex cytochrome c subunit: CL
CYTOCHROME AA3 SUBUNIT CtaC: DM
Probable cytochrome c oxidase subunit 1: EN
Probable cytochrome c oxidase subunit 3: FO
Cytochrome c oxidase polypeptide 4: GP
CYTOCHROME AA3 SUBUNIT CtaJ: HQ
DUF5130 domain-containing protein: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
M

B
B

K
N

C
C

L
O

D
E

M
Q

E
F

N
R

F
G

O
S

G
H

P
T

H
I

Q
U

I
J

R
V

Membrane

We predict this structure to be a membrane protein.
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Cytochrome bc1 complex Rieske iron-sulfur subunit

Cytochrome bc1 complex cytochrome b subunit

Cytochrome bc1 complex cytochrome c subunit

CYTOCHROME AA3 SUBUNIT CtaC

Probable cytochrome c oxidase subunit 1

Probable cytochrome c oxidase subunit 3

Cytochrome c oxidase polypeptide 4

CYTOCHROME AA3 SUBUNIT CtaJ

DUF5130 domain-containing protein

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