SMTL ID : 7rja.1

Complex III2 from Candida albicans, inhibitor free

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

HEM.1: 30 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, L.190, E.272, Y.274 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.40, B:Q.43, B:Q.43, B:I.44, B:L.50, B:A.51, B:A.86, B:F.89, B:F.89, B:I.127, B:L.134, B:L.134, B:V.135, B:F.180, B:F.184, B:F.184, B:P.187, B:L.190 Salt bridges: B:R.79, B:R.79 Metal complexes: B:H.183 HEM.2: 30 residues within 4Å: Chain B: W.29, W.30, G.33, S.34, L.36, G.37, L.40, F.89, M.93, H.96, I.97, K.99, A.100, S.105, 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, L.302 Ligands: U10.4 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:L.36, B:F.89, B:I.97, B:L.113, B:W.114, B:W.114, B:F.121, 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-Stacking: B:H.197 Metal complexes: B:H.96, B:H.197 HEM.7: 31 residues within 4Å: Chain K: 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 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:L.40, K:Q.43, K:Q.43, K:I.44, K:L.50, K:A.51, K:A.86, K:I.127, K:L.134, K:L.134, K:V.135, K:F.180, K:F.184, K:P.187, K:L.190 Salt bridges: K:R.79, K:R.79 Metal complexes: K:H.183 HEM.8: 30 residues within 4Å: Chain K: W.29, W.30, G.33, S.34, L.36, G.37, L.40, F.89, M.93, H.96, I.97, K.99, A.100, S.105, 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, L.302 Ligands: U10.10 23 PLIP interactions: 23 interactions with chain K, Hydrophobic interactions: K:L.36, K:F.89, K:I.97, K:I.97, K:A.100, K:L.113, K:W.114, K:F.121, K:V.194, K:V.194, K:L.198, K:L.201 Hydrogen bonds: K:W.30, K:G.33, K:S.105, K:S.207 Salt bridges: K:H.96, K:K.99, K:K.99, K:R.110 pi-Stacking: K:H.197 Metal complexes: K:H.96, K:H.197

4 x U10: UBIQUINONE-10(Non-covalent)(Covalent)

U10.3: 20 residues within 4Å: Chain B: I.122, L.123, M.125, A.126, F.129, Y.132, G.143, A.144, V.146, I.147, L.186, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, F.296, I.299 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.122, B:L.123, B:M.125, B:A.126, B:I.147, B:L.275, B:L.282, B:F.296 U10.4: 20 residues within 4Å: Chain B: Y.16, L.17, S.20, Q.22, I.26, W.30, G.33, S.34, G.37, L.38, L.40, V.41, V.194, L.198, L.201, S.206, M.221, F.225, D.229 Ligands: HEM.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.16, B:L.17 U10.9: 19 residues within 4Å: Chain K: I.122, L.123, M.125, A.126, F.129, Y.132, G.143, V.146, I.147, L.150, L.186, I.269, P.271, L.275, F.278, Y.279, L.282, M.295, F.296 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:I.122, K:L.123, K:A.126, K:I.147, K:L.275, K:F.296 U10.10: 19 residues within 4Å: Chain K: Y.16, L.17, S.20, Q.22, I.26, W.30, G.33, S.34, G.37, L.40, V.41, V.194, L.198, L.201, S.206, M.221, F.225, D.229 Ligands: HEM.8 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.16

2 x HEC: HEME C(Covalent)

HEC.5: 27 residues within 4Å: Chain C: 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, V.232, L.236 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:V.81, C:N.150, C:P.155, C:P.156, C:I.161, C:I.172, C:L.176, C:V.232, C:L.236 Hydrogen bonds: C:Y.171, C:A.205 Salt bridges: C:R.165 pi-Cation interactions: C:H.86 Metal complexes: C:H.86 HEC.11: 27 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, V.232, L.236 15 PLIP interactions: 15 interactions with chain L, Hydrophobic interactions: L:V.81, L:N.150, L:P.155, L:P.156, L:L.158, L:I.161, L:I.172, L:L.175, L:F.199, L:V.232, L:L.236 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.6: 8 residues within 4Å: Chain H: C.156, T.157, H.158, L.159, C.175, C.177, H.178, P.192 2 PLIP interactions: 2 interactions with chain H, Metal complexes: H:H.158, H:H.158 FES.12: 6 residues within 4Å: Chain Q: C.156, H.158, L.159, C.175, C.177, H.178 2 PLIP interactions: 2 interactions with chain Q, Metal complexes: Q:H.158, Q: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

Ubiquinol--cytochrome-c reductase subunit: AJ
Cytochrome b: BK
Ubiquinol--cytochrome-c reductase catalytic subunit: CL
Cytochrome b-c1 complex subunit 7: DM
Ubiquinol--cytochrome-c reductase subunit 8: EN
Ubiquinol--cytochrome-c reductase subunit 6: FO
Ubiquinol--cytochrome-c reductase subunit 9: GP
Cytochrome b-c1 complex subunit Rieske, mitochondrial: HQ
Cytochrome b-c1 complex subunit 2, mitochondrial: IR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
J

B
K

K
T

C
D

L
N

D
G

M
Q

E
F

N
P

F
H

O
R

G
I

P
S

H
C

Q
M

I
B

R
L

Membrane

We predict this structure to be a membrane protein.
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Ubiquinol--cytochrome-c reductase subunit

Cytochrome b

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

Cytochrome b-c1 complex subunit 2, mitochondrial

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