- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.30 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PC1.3: 14 residues within 4Å:- Chain A: F.29, Y.94, Y.102, Y.103, A.317, F.326, G.327, I.330, C.331
- Chain C: L.40
- Chain H: Q.53, F.56, V.57
- Ligands: CDL.16
8 PLIP interactions:7 interactions with chain A, 1 interactions with chain H- Hydrophobic interactions: A:Y.102, A:Y.102, A:F.326, A:I.330, A:I.330, H:F.56
- Hydrogen bonds: A:Y.103
- Salt bridges: A:K.323
PC1.18: 16 residues within 4Å:- Chain E: D.445, S.470, M.472
- Chain I: Y.8, V.12, K.13, N.15, F.18, V.19, I.22
- Chain L: Y.66, G.73, S.76, A.77
- Ligands: PTY.4, CDL.11
5 PLIP interactions:2 interactions with chain I, 2 interactions with chain L, 1 interactions with chain E- Hydrophobic interactions: I:I.22, L:A.77
- Hydrogen bonds: I:N.15
- pi-Cation interactions: L:Y.66
- Salt bridges: E:D.445
PC1.22: 14 residues within 4Å:- Chain K: F.29, Y.94, G.98, Y.102, Y.103, A.317, F.326, G.327, I.330
- Chain M: L.40
- Chain R: Q.53, F.56, V.57
- Ligands: CDL.23
10 PLIP interactions:9 interactions with chain K, 1 interactions with chain R- Hydrophobic interactions: K:F.29, K:F.29, K:Y.102, K:Y.102, K:F.326, K:I.330, K:I.330, R:F.56
- Hydrogen bonds: K:Y.103
- Salt bridges: K:K.323
PC1.35: 17 residues within 4Å:- Chain B: Y.66, I.69, G.73, S.76
- Chain O: D.445, S.470, M.472
- Chain S: Y.8, V.12, K.13, N.15, F.18, V.19, I.22, L.23
- Ligands: PTY.24, CDL.30
7 PLIP interactions:1 interactions with chain O, 5 interactions with chain S, 1 interactions with chain B- Salt bridges: O:D.445
- Hydrophobic interactions: S:V.19, S:V.19, S:I.22, S:L.23
- Hydrogen bonds: S:N.15
- pi-Cation interactions: B:Y.66
- 4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)
PTY.4: 18 residues within 4Å:- Chain A: S.34, A.37, L.38, H.222, S.226, F.227, D.229, L.230, V.233, F.234
- Chain E: N.467
- Chain G: K.314
- Chain L: I.69, F.72, S.76
- Ligands: AWB.7, CDL.11, PC1.18
13 PLIP interactions:8 interactions with chain A, 2 interactions with chain L, 1 interactions with chain E, 2 interactions with chain G- Hydrophobic interactions: A:A.37, A:F.227, A:D.229, A:L.230, A:V.233, A:F.234, L:F.72, L:F.72
- Salt bridges: A:H.222, A:H.222, G:K.314, G:K.314
- Hydrogen bonds: E:N.467
PTY.10: 20 residues within 4Å:- Chain B: G.79, A.80, K.81, A.82, T.83, V.84, Q.85, D.86, F.87
- Chain K: F.77, L.237, F.240, F.245
- Chain Q: L.292, K.295, A.296, V.299, I.300
- Chain S: D.30
- Ligands: LMT.36
8 PLIP interactions:2 interactions with chain K, 2 interactions with chain Q, 1 interactions with chain S, 3 interactions with chain B- Hydrophobic interactions: K:L.237, K:F.240, Q:I.300, B:V.84, B:F.87
- Salt bridges: Q:K.295
- Hydrogen bonds: S:D.30, B:K.81
PTY.15: 19 residues within 4Å:- Chain A: F.77, L.237, F.240, F.245
- Chain G: L.292, K.295, A.296, V.299, I.300
- Chain I: D.30
- Chain L: G.79, A.80, K.81, A.82, T.83, V.84, Q.85, D.86
- Ligands: LMT.19
8 PLIP interactions:3 interactions with chain L, 2 interactions with chain G, 1 interactions with chain I, 2 interactions with chain A- Hydrophobic interactions: L:V.84, G:I.300, A:F.77, A:L.237
- Hydrogen bonds: L:K.81, L:D.86, I:D.30
- Salt bridges: G:K.295
PTY.24: 19 residues within 4Å:- Chain B: I.69, F.72, S.76
- Chain K: S.34, A.37, L.38, H.222, P.223, S.226, F.227, D.229, L.230, F.234
- Chain O: N.467, M.472
- Chain Q: K.314
- Ligands: AWB.27, CDL.30, PC1.35
12 PLIP interactions:1 interactions with chain Q, 8 interactions with chain K, 2 interactions with chain B, 1 interactions with chain O- Salt bridges: Q:K.314, K:H.222, K:H.222
- Hydrophobic interactions: K:A.37, K:L.38, K:F.227, K:D.229, K:L.230, K:F.234, B:F.72, B:F.72
- Hydrogen bonds: O:N.467
- 10 x CDL: CARDIOLIPIN(Non-covalent)
CDL.5: 13 residues within 4Å:- Chain A: T.108, P.109, R.110, V.111, L.112, S.115, L.303, P.306, I.307
- Chain K: L.3, K.6, N.7, L.10
7 PLIP interactions:1 interactions with chain K, 6 interactions with chain A- Hydrogen bonds: K:N.7, A:T.108, A:P.109, A:V.111, A:L.112
- Hydrophobic interactions: A:V.111, A:I.307
CDL.11: 14 residues within 4Å:- Chain A: R.4, H.222, S.226
- Chain E: H.364, K.368, M.471, M.472, R.473
- Chain J: W.38
- Ligands: PTY.4, AWB.7, CDL.12, XP4.13, PC1.18
10 PLIP interactions:2 interactions with chain A, 7 interactions with chain E, 1 interactions with chain J- Salt bridges: A:R.4, A:H.222, E:H.364, E:K.368, E:R.473
- Hydrogen bonds: E:H.364, E:M.472, E:R.473, E:R.473
- Hydrophobic interactions: J:W.38
CDL.12: 9 residues within 4Å:- Chain A: L.3, L.10, V.17
- Chain E: H.364, F.365, R.372, R.473
- Ligands: CDL.11, XP4.13
8 PLIP interactions:3 interactions with chain A, 5 interactions with chain E- Hydrophobic interactions: A:L.10, A:V.17
- Hydrogen bonds: A:L.3, E:R.473
- Salt bridges: E:H.364, E:R.372, E:R.473, E:R.473
CDL.16: 17 residues within 4Å:- Chain A: N.27, Y.28, F.29, F.32, L.35, T.232, A.235, F.236, M.239
- Chain C: H.84
- Chain H: R.49, T.50, Q.53, A.54, V.57
- Ligands: PC1.3, CDL.17
13 PLIP interactions:6 interactions with chain H, 6 interactions with chain A, 1 interactions with chain C- Hydrophobic interactions: H:T.50, H:V.57, A:Y.28, A:F.32, A:T.232, A:A.235
- Hydrogen bonds: H:Q.53, A:N.27, A:Y.28
- Salt bridges: H:R.49, H:R.49, H:R.49, C:H.84
CDL.17: 13 residues within 4Å:- Chain A: Y.28
- Chain C: H.84
- Chain G: V.308, K.311, K.312, K.319
- Chain H: V.38, A.41, A.42, N.45, T.46, R.49
- Ligands: CDL.16
8 PLIP interactions:5 interactions with chain H, 3 interactions with chain G- Hydrophobic interactions: H:V.38
- Hydrogen bonds: H:N.45, H:R.49, H:R.49
- Salt bridges: H:R.49, G:K.311, G:K.312, G:K.319
CDL.23: 16 residues within 4Å:- Chain K: N.27, Y.28, F.29, F.32, L.35, Y.103, T.232, F.236, M.239
- Chain M: H.84
- Chain R: R.49, T.50, Q.53, V.57
- Ligands: PC1.22, CDL.34
12 PLIP interactions:5 interactions with chain R, 6 interactions with chain K, 1 interactions with chain M- Hydrophobic interactions: R:T.50, R:V.57, K:Y.28, K:F.32, K:L.35, K:T.232
- Salt bridges: R:R.49, R:R.49, R:R.49, M:H.84
- Hydrogen bonds: K:Y.28, K:Y.103
CDL.25: 12 residues within 4Å:- Chain A: L.3, K.6, N.7, L.10
- Chain K: T.108, P.109, R.110, V.111, L.112, S.115, L.303, P.306
7 PLIP interactions:1 interactions with chain A, 6 interactions with chain K- Hydrogen bonds: A:N.7, K:T.108, K:P.109, K:P.109, K:V.111, K:L.112
- Hydrophobic interactions: K:V.111
CDL.30: 15 residues within 4Å:- Chain K: R.4, V.17, H.222, S.226
- Chain O: H.364, K.368, M.471, M.472, R.473
- Chain T: W.38
- Ligands: PTY.24, AWB.27, CDL.31, XP4.32, PC1.35
11 PLIP interactions:7 interactions with chain O, 4 interactions with chain K- Hydrogen bonds: O:H.364, O:M.472, O:R.473, O:R.473
- Salt bridges: O:H.364, O:K.368, O:R.473, K:R.4, K:H.222
- Hydrophobic interactions: K:V.17, K:V.17
CDL.31: 9 residues within 4Å:- Chain K: L.3, L.10, V.17
- Chain O: H.364, F.365, R.372, R.473
- Ligands: CDL.30, XP4.32
8 PLIP interactions:5 interactions with chain O, 3 interactions with chain K- Hydrogen bonds: O:R.473, K:L.3
- Salt bridges: O:H.364, O:R.372, O:R.473, O:R.473
- Hydrophobic interactions: K:L.10, K:V.17
CDL.34: 13 residues within 4Å:- Chain K: Y.28
- Chain M: H.84
- Chain Q: V.308, K.311, K.312, K.319
- Chain R: V.38, A.41, A.42, N.45, T.46, R.49
- Ligands: CDL.23
8 PLIP interactions:5 interactions with chain R, 3 interactions with chain Q- Hydrophobic interactions: R:V.38
- Hydrogen bonds: R:N.45, R:R.49, R:R.49
- Salt bridges: R:R.49, Q:K.311, Q:K.312, Q:K.319
- 4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.6: 11 residues within 4Å:- Chain A: N.11, M.12, S.15, Y.16, L.195, I.199, H.202
- Chain H: W.10
- Chain K: M.12
- Ligands: AWB.7, LMT.26
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:M.12, A:Y.16, A:L.195, A:L.195, A:I.199
- Hydrogen bonds: A:N.11, A:N.11, A:N.11, A:S.15, A:Y.16
LMT.19: 13 residues within 4Å:- Chain A: F.74
- Chain G: E.288, L.292
- Chain J: L.49, I.50, G.52, V.53, R.57
- Chain L: Q.85, D.86, L.88, S.89
- Ligands: PTY.15
14 PLIP interactions:6 interactions with chain L, 7 interactions with chain J, 1 interactions with chain G- Hydrophobic interactions: L:Q.85, L:L.88, J:L.49, J:L.49, J:I.50, J:V.53
- Hydrogen bonds: L:Q.85, L:D.86, L:D.86, L:S.89, J:G.52, J:R.57, J:R.57, G:E.288
LMT.26: 10 residues within 4Å:- Chain A: M.12
- Chain K: N.11, M.12, S.15, Y.16, I.199, H.202
- Chain R: W.10
- Ligands: LMT.6, AWB.27
8 PLIP interactions:8 interactions with chain K- Hydrophobic interactions: K:M.12, K:Y.16, K:I.199
- Hydrogen bonds: K:N.11, K:N.11, K:N.11, K:S.15, K:Y.16
LMT.36: 10 residues within 4Å:- Chain B: Q.85, D.86, S.89
- Chain K: F.74
- Chain Q: E.288, L.292
- Chain T: G.52, V.53, R.57
- Ligands: PTY.10
10 PLIP interactions:5 interactions with chain B, 4 interactions with chain T, 1 interactions with chain Q- Hydrophobic interactions: B:Q.85, T:V.53
- Hydrogen bonds: B:Q.85, B:D.86, B:D.86, B:S.89, T:G.52, T:R.57, T:R.57, Q:E.288
- 2 x AWB: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate(Non-covalent)
AWB.7: 21 residues within 4Å:- Chain A: Y.16, V.17, Q.22, L.26, W.30, N.31, S.34, A.37, L.40, A.194, L.195, L.198, S.206, M.221, Y.225, K.228, D.229
- Ligands: HEM.2, PTY.4, LMT.6, CDL.11
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:L.26, A:A.37, A:L.40, A:A.194
- Hydrogen bonds: A:K.228, A:D.229
AWB.27: 23 residues within 4Å:- Chain K: A.13, Y.16, V.17, Q.22, L.26, W.30, N.31, S.34, A.37, L.40, A.191, A.194, L.195, L.198, S.206, M.221, Y.225, K.228, D.229
- Ligands: HEM.21, PTY.24, LMT.26, CDL.30
8 PLIP interactions:8 interactions with chain K- Hydrophobic interactions: K:A.13, K:L.26, K:A.37, K:L.40, K:A.194, K:L.195
- Hydrogen bonds: K:K.228, K:D.229
- 2 x AOQ: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione(Non-covalent)
AOQ.8: 16 residues within 4Å:- Chain A: L.122, I.125, F.129, M.139, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, M.295, I.299
- Chain B: C.189, H.190
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:I.125, A:I.125, A:F.129, A:I.147, A:I.269, A:I.269, A:P.271, A:L.275, A:F.278, A:F.278, A:Y.279, A:I.299
AOQ.28: 15 residues within 4Å:- Chain K: L.122, I.125, F.129, M.139, G.143, V.146, I.147, I.269, P.271, L.275, F.278, Y.279, M.295, I.299
- Chain L: H.190
12 PLIP interactions:12 interactions with chain K- Hydrophobic interactions: K:I.125, K:I.125, K:F.129, K:V.146, K:I.147, K:I.269, K:P.271, K:L.275, K:F.278, K:F.278, K:Y.279, K:I.299
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.9: 10 residues within 4Å:- Chain B: C.168, H.170, L.171, G.172, C.173, C.187, C.189, H.190, G.191, S.192
4 PLIP interactions:4 interactions with chain B,- Metal complexes: B:C.168, B:H.170, B:C.187, B:H.190
FES.29: 10 residues within 4Å:- Chain L: C.168, H.170, L.171, G.172, C.173, C.187, C.189, H.190, G.191, S.192
4 PLIP interactions:4 interactions with chain L,- Metal complexes: L:C.168, L:H.170, L:C.187, L:H.190
- 2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)
XP4.13: 11 residues within 4Å:- Chain E: R.372, S.376, R.473
- Chain J: F.23, T.27, V.28, W.31, F.35, W.38
- Ligands: CDL.11, CDL.12
9 PLIP interactions:6 interactions with chain J, 3 interactions with chain E- Hydrophobic interactions: J:F.23, J:W.31, J:F.35, J:W.38, J:W.38, J:W.38, E:R.473
- Hydrogen bonds: E:S.376
- Salt bridges: E:R.372
XP4.32: 11 residues within 4Å:- Chain O: R.372, S.376, R.473
- Chain T: F.23, T.27, V.28, W.31, F.35, W.38
- Ligands: CDL.30, CDL.31
8 PLIP interactions:3 interactions with chain O, 5 interactions with chain T- Hydrophobic interactions: O:R.473, T:W.31, T:F.35, T:W.38, T:W.38, T:W.38
- Hydrogen bonds: O:S.376
- Salt bridges: O:R.372
- 2 x HEC: HEME C(Non-covalent)
HEC.14: 24 residues within 4Å:- Chain G: V.119, V.123, C.124, C.127, H.128, N.192, A.195, L.196, P.197, P.198, L.200, I.203, R.207, Y.213, I.214, L.217, L.218, F.241, I.246, G.247, M.248, T.251, V.274, L.278
23 PLIP interactions:23 interactions with chain G,- Hydrophobic interactions: G:V.119, G:V.123, G:N.192, G:A.195, G:P.197, G:P.197, G:L.200, G:I.203, G:I.214, G:L.217, G:L.218, G:L.218, G:F.241, G:I.246, G:M.248, G:T.251, G:V.274, G:L.278
- Hydrogen bonds: G:Y.213, G:Y.213, G:G.247
- Salt bridges: G:R.207
- Metal complexes: G:H.128
HEC.33: 24 residues within 4Å:- Chain Q: V.119, V.123, C.124, C.127, H.128, N.192, A.195, L.196, P.197, P.198, L.200, I.203, R.207, Y.213, I.214, L.217, L.218, F.241, I.246, G.247, M.248, T.251, V.274, L.278
23 PLIP interactions:23 interactions with chain Q,- Hydrophobic interactions: Q:V.119, Q:V.123, Q:N.192, Q:A.195, Q:P.197, Q:P.197, Q:L.200, Q:I.203, Q:I.214, Q:L.217, Q:L.218, Q:L.218, Q:F.241, Q:I.246, Q:M.248, Q:T.251, Q:V.274, Q:L.278
- Hydrogen bonds: Q:Y.213, Q:Y.213, Q:G.247
- Salt bridges: Q:R.207
- Metal complexes: Q:H.128
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wieferig, J.P. et al., Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. Iucrj (2023)
- Release Date
- 2023-01-11
- Peptides
- Cytochrome b: AK
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BL
Cytochrome b-c1 complex subunit 7: CM
YALI0F24673p: DN
YALI0A14806p: EO
Cytochrome b-c1 complex subunit 2, mitochondrial: FP
YALI0A17468p: GQ
Cytochrome b-c1 complex subunit 8: HR
Complex III subunit 9: IS
YALI0C12210p: JT - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CK
NB
PL
EC
GM
RD
FN
QE
AO
LF
BP
MG
DQ
OH
HR
SI
IS
TJ
JT
U - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.30 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)
- 10 x CDL: CARDIOLIPIN(Non-covalent)
- 4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 2 x AWB: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate(Non-covalent)
- 2 x AOQ: 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)
- 2 x HEC: HEME C(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wieferig, J.P. et al., Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. Iucrj (2023)
- Release Date
- 2023-01-11
- Peptides
- Cytochrome b: AK
Cytochrome b-c1 complex subunit Rieske, mitochondrial: BL
Cytochrome b-c1 complex subunit 7: CM
YALI0F24673p: DN
YALI0A14806p: EO
Cytochrome b-c1 complex subunit 2, mitochondrial: FP
YALI0A17468p: GQ
Cytochrome b-c1 complex subunit 8: HR
Complex III subunit 9: IS
YALI0C12210p: JT - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CK
NB
PL
EC
GM
RD
FN
QE
AO
LF
BP
MG
DQ
OH
HR
SI
IS
TJ
JT
U - Membrane
-
We predict this structure to be a membrane protein.