SMTL ID : 7rje.1

Complex III2 from Candida albicans, Inz-5 bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 31 residues within 4Å: Chain A: L.40, Q.43, I.44, G.47, V.48, L.50, A.51, Y.54, V.65, I.68, R.79, H.82, A.83, A.86, F.89, F.90, T.124, I.127, A.128, G.131, Y.132, L.134, V.135, F.180, H.183, F.184, P.187, L.190, E.272, Y.274 Ligands: ZL5.3 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:L.40, A:V.48, A:L.50, A:L.50, A:Y.54, A:A.83, A:A.86, A:I.127, A:Y.132, A:L.134, A:V.135, A:F.184, A:F.184, A:P.187 Salt bridges: A:R.79, A:R.79 pi-Cation interactions: A:H.82 Metal complexes: A:H.82 HEM.2: 29 residues within 4Å: Chain A: W.30, N.31, L.32, G.33, S.34, L.36, G.37, F.89, M.93, H.96, I.97, K.99, A.100, S.105, Y.106, R.110, L.113, W.114, G.117, V.118, I.120, F.121, L.190, V.194, H.197, L.198, L.201, S.206, S.207 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.36, A:L.36, A:F.89, A:I.97, A:A.100, A:L.113, A:W.114, A:W.114, A:V.194, A:V.194, A:L.198, A:L.201 Hydrogen bonds: A:W.30, A:G.33, A:S.105, A:S.207 Salt bridges: A:H.96, A:K.99, A:K.99, A:R.110 pi-Cation interactions: A:K.99, A:H.197 Metal complexes: A:H.197 HEM.4: 32 residues within 4Å: Chain B: L.40, Q.43, I.44, G.47, V.48, L.50, A.51, Y.54, V.65, I.68, R.79, H.82, A.83, A.86, F.89, F.90, T.124, I.127, A.128, G.131, Y.132, L.134, V.135, F.180, H.183, F.184, P.187, F.188, L.190, E.272, Y.274 Ligands: ZL5.6 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:L.40, B:L.50, B:L.50, B:Y.54, B:A.83, B:A.86, B:I.127, B:Y.132, B:L.134, B:V.135, B:F.184, B:F.184, B:P.187 Salt bridges: B:R.79, B:R.79 pi-Cation interactions: B:H.82 Metal complexes: B:H.82 HEM.5: 29 residues within 4Å: Chain B: W.30, L.32, G.33, S.34, L.36, G.37, F.89, M.93, H.96, I.97, K.99, A.100, S.105, Y.106, R.110, L.113, W.114, G.117, V.118, I.120, F.121, T.124, L.190, V.194, H.197, L.198, L.201, S.206, S.207 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:L.36, B:L.36, B:F.89, B:I.97, B:A.100, B:L.113, B:W.114, B:W.114, B:V.194, B:V.194, B:L.198, B:L.201 Hydrogen bonds: B:W.30, B:G.33, B:S.105, B:S.207 Salt bridges: B:H.96, B:K.99, B:K.99, B:R.110 pi-Cation interactions: B:K.99, B:H.197 Metal complexes: B:H.197

2 x ZL5: 3-[2-fluoro-5-(trifluoromethyl)phenyl]-7-methyl-1-[(2-methyl-2H-tetrazol-5-yl)methyl]-1H-indazole(Non-covalent)

ZL5.3: 22 residues within 4Å: Chain A: M.125, A.126, A.128, F.129, Y.132, C.133, M.139, G.143, V.146, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, F.278, Y.279, L.282, M.295, F.296 Ligands: HEM.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.129, A:I.147, A:I.147, A:I.269, A:Y.279, A:Y.279 Hydrogen bonds: A:E.272 Salt bridges: A:E.272 ZL5.6: 21 residues within 4Å: Chain B: M.125, A.126, A.128, F.129, Y.132, C.133, M.139, G.143, V.146, I.147, I.269, V.270, P.271, E.272, Y.274, L.275, F.278, Y.279, M.295, F.296 Ligands: HEM.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.129, B:I.147, B:I.269, B:Y.279, B:Y.279 Hydrogen bonds: B:E.272 Salt bridges: B:E.272

2 x HEC: HEME C(Covalent)

HEC.7: 28 residues within 4Å: Chain E: V.77, Y.78, V.81, C.82, A.84, C.85, H.86, N.150, A.153, Y.154, P.155, P.156, L.158, I.161, R.165, Y.171, I.172, L.175, L.176, F.199, P.200, I.204, A.205, M.206, V.209, L.210, V.232, L.236 19 PLIP interactions: 19 interactions with chain E, Hydrophobic interactions: E:V.81, E:N.150, E:A.153, E:P.155, E:P.155, E:P.156, E:I.161, E:I.172, E:L.175, E:L.176, E:F.199, E:A.205, E:V.209, E:V.209, E:V.232 Hydrogen bonds: E:Y.171, E:A.205 Salt bridges: E:R.165 Metal complexes: E:H.86 HEC.8: 28 residues within 4Å: Chain L: V.77, Y.78, V.81, C.82, A.84, C.85, H.86, N.150, A.153, Y.154, P.155, P.156, L.158, I.161, R.165, Y.171, I.172, L.175, L.176, F.199, P.200, I.204, A.205, M.206, V.209, L.210, V.232, L.236 18 PLIP interactions: 18 interactions with chain L, Hydrophobic interactions: L:V.81, L:N.150, L:A.153, L:P.155, L:P.155, L:P.156, L:I.161, L:L.175, L:L.176, L:F.199, L:A.205, L:V.209, L:V.209, L:V.232 Hydrogen bonds: L:Y.171, L:A.205 Salt bridges: L:R.165 Metal complexes: L:H.86

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

FES.9: 8 residues within 4Å: Chain Q: C.156, T.157, H.158, L.159, C.175, C.177, H.178, P.192 2 PLIP interactions: 2 interactions with chain Q, Metal complexes: Q:H.158, Q:H.158 FES.10: 6 residues within 4Å: Chain R: C.156, H.158, L.159, C.175, C.177, H.178 2 PLIP interactions: 2 interactions with chain R, Metal complexes: R:H.158, R:H.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Trani, J.M. et al., Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III. Structure (2022)

Release Date

2021-09-15

Peptides

Cytochrome b: AB
Ubiquinol--cytochrome-c reductase subunit: CJ
Cytochrome b-c1 complex subunit 2, mitochondrial: DK
Ubiquinol--cytochrome-c reductase catalytic subunit: EL
Cytochrome b-c1 complex subunit 7: FM
Ubiquinol--cytochrome-c reductase subunit 8: GN
Ubiquinol--cytochrome-c reductase subunit 6: HO
Ubiquinol--cytochrome-c reductase subunit 9: IP
Cytochrome b-c1 complex subunit Rieske, mitochondrial: QR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
T

C
A

J
E

D
B

K
L

E
D

L
N

F
G

M
P

G
F

N
O

H
H

O
Q

I
I

P
R

Q
C

R
M

Membrane

We predict this structure to be a membrane protein.
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Cytochrome b

Ubiquinol--cytochrome-c reductase subunit

Cytochrome b-c1 complex subunit 2, mitochondrial

Ubiquinol--cytochrome-c reductase catalytic subunit

Cytochrome b-c1 complex subunit 7

Ubiquinol--cytochrome-c reductase subunit 8

Ubiquinol--cytochrome-c reductase subunit 6

Ubiquinol--cytochrome-c reductase subunit 9

Cytochrome b-c1 complex subunit Rieske, mitochondrial

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