- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.70 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: 13 residues within 4Å:- Chain A: F.29, Y.94, Y.102, Y.103, A.317, G.327, I.330
- Chain C: L.40, L.86
- Chain H: Q.53, F.56, V.57
- Ligands: CDL.15
8 PLIP interactions:1 interactions with chain H, 7 interactions with chain A- Hydrophobic interactions: H:F.56, A:F.29, A:F.29, A:Y.102, A:Y.102, A:I.330
- Hydrogen bonds: A:Y.103
- Salt bridges: A:K.323
PC1.16: 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.80
- Ligands: PTY.4, CDL.10
4 PLIP interactions:1 interactions with chain E, 1 interactions with chain L, 2 interactions with chain I- Salt bridges: E:D.445
- Hydrophobic interactions: L:A.80, I:I.22
- Hydrogen bonds: I:N.15
PC1.20: 12 residues within 4Å:- Chain K: F.29, Y.94, Y.102, Y.103, A.317, G.327, I.330
- Chain M: L.40
- Chain R: Q.53, F.56, V.57
- Ligands: CDL.21
7 PLIP interactions:6 interactions with chain K, 1 interactions with chain R- Hydrophobic interactions: K:Y.102, K:Y.102, K:I.330, K:I.330, R:F.56
- Hydrogen bonds: K:Y.103
- Salt bridges: K:K.323
PC1.31: 17 residues within 4Å:- Chain B: Y.66, G.73, S.76, A.77
- 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.22, CDL.26
6 PLIP interactions:1 interactions with chain B, 4 interactions with chain S, 1 interactions with chain O- Hydrophobic interactions: B:A.77, S:V.19, S:I.22, S:L.23
- Hydrogen bonds: S:N.15
- Salt bridges: O:D.445
- 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.6, CDL.10, PC1.16
14 PLIP interactions:2 interactions with chain L, 9 interactions with chain A, 2 interactions with chain G, 1 interactions with chain E- Hydrophobic interactions: L:F.72, L:F.72, A:A.37, A:L.38, A:F.227, A:D.229, A:L.230, A:V.233, A:F.234
- Salt bridges: A:H.222, A:H.222, G:K.314, G:K.314
- Hydrogen bonds: E:S.470
PTY.9: 18 residues within 4Å:- Chain B: G.79, A.80, K.81, A.82, T.83, V.84, Q.85, D.86
- Chain K: F.77, L.237, F.245
- Chain Q: L.292, K.295, A.296, V.299, I.300
- Chain S: D.30
- Ligands: LMT.8
6 PLIP interactions:2 interactions with chain Q, 2 interactions with chain K, 1 interactions with chain S, 1 interactions with chain B- Hydrophobic interactions: Q:I.300, K:F.77, K:L.237, B:V.84
- Salt bridges: Q:K.295
- Hydrogen bonds: S:D.30
PTY.22: 18 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
- Chain O: N.467, M.472
- Chain Q: K.314
- Ligands: AWB.24, CDL.26, PC1.31
10 PLIP interactions:1 interactions with chain B, 7 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain O- Hydrophobic interactions: B:F.72, K:A.37, K:L.38, K:F.227, K:D.229, K:L.230
- Salt bridges: K:H.222, K:H.222, Q:K.314
- Hydrogen bonds: O:N.467
PTY.25: 18 residues within 4Å:- Chain A: F.77, 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.17
10 PLIP interactions:3 interactions with chain G, 1 interactions with chain I, 2 interactions with chain A, 4 interactions with chain L- Hydrophobic interactions: G:V.299, G:I.300, A:F.77, A:F.240, L:A.80, L:V.84
- Salt bridges: G:K.295
- Hydrogen bonds: I:D.30, L:K.81, L:D.86
- 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, I.307
- Chain H: Y.7
- Chain K: L.3, K.6, N.7, L.10
9 PLIP interactions:7 interactions with chain A, 2 interactions with chain K- Hydrophobic interactions: A:V.111, A:L.303, A:I.307
- Hydrogen bonds: A:T.108, A:P.109, A:V.111, A:L.112, K:N.7
- Salt bridges: K:K.6
CDL.10: 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.6, CDL.11, XP4.12, PC1.16
10 PLIP interactions:1 interactions with chain J, 7 interactions with chain E, 2 interactions with chain A- Hydrophobic interactions: J:W.38
- Hydrogen bonds: E:H.364, E:M.472, E:R.473, E:R.473
- Salt bridges: E:H.364, E:K.368, E:R.473, A:R.4, A:H.222
CDL.11: 8 residues within 4Å:- Chain A: A.2, L.3
- Chain E: H.364, F.365, R.372, R.473
- Ligands: CDL.10, XP4.12
6 PLIP interactions:5 interactions with chain E, 1 interactions with chain A- Hydrogen bonds: E:R.473, A:L.3
- Salt bridges: E:H.364, E:R.372, E:R.473, E:R.473
CDL.14: 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.15
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.15: 14 residues within 4Å:- Chain A: N.27, Y.28, F.29, F.32, L.35, T.232, F.236, M.239
- Chain C: H.84
- Chain H: R.49, T.50, Q.53
- Ligands: PC1.3, CDL.14
13 PLIP interactions:7 interactions with chain A, 5 interactions with chain H, 1 interactions with chain C- Hydrophobic interactions: A:Y.28, A:F.29, A:F.32, A:L.35, A:T.232, H:T.50
- Hydrogen bonds: A:N.27, A:Y.28, H:Q.53
- Salt bridges: H:R.49, H:R.49, H:R.49, C:H.84
CDL.21: 14 residues within 4Å:- Chain K: N.27, Y.28, F.29, F.32, L.35, Y.103, T.232, M.239
- Chain M: H.84
- Chain R: R.49, T.50, Q.53
- Ligands: PC1.20, CDL.30
12 PLIP interactions:6 interactions with chain K, 4 interactions with chain R, 2 interactions with chain M- Hydrophobic interactions: K:Y.28, K:F.32, K:L.35, K:T.232, R:T.50
- Hydrogen bonds: K:Y.28, K:Y.103, M:H.84
- Salt bridges: R:R.49, R:R.49, R:R.49, M:H.84
CDL.23: 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, I.307
7 PLIP interactions:5 interactions with chain K, 2 interactions with chain A- Hydrophobic interactions: K:V.111
- Hydrogen bonds: K:T.108, K:P.109, K:V.111, K:L.112, A:N.7
- Salt bridges: A:K.6
CDL.26: 13 residues within 4Å:- Chain K: R.4, H.222
- Chain O: H.364, K.368, M.471, M.472, R.473
- Chain S: N.15
- Ligands: PTY.22, AWB.24, CDL.27, XP4.28, PC1.31
9 PLIP interactions:7 interactions with chain O, 2 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
CDL.27: 7 residues within 4Å:- Chain K: L.3
- Chain O: H.364, F.365, R.372, R.473
- Ligands: CDL.26, XP4.28
6 PLIP interactions:5 interactions with chain O, 1 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
CDL.30: 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.21
9 PLIP interactions:5 interactions with chain R, 3 interactions with chain Q, 1 interactions with chain K- Hydrophobic interactions: R:V.38, K:Y.28
- 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
- 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.6: 20 residues within 4Å:- Chain A: 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, M.221, Y.225, D.229
- Ligands: HEM.2, PTY.4, CDL.10
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:A.13, A:V.17, A:L.26, A:A.37, A:L.40, A:A.194, A:L.198
- Hydrogen bonds: A:S.34, A:D.229
AWB.24: 20 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, M.221, Y.225, D.229
- Ligands: HEM.19, PTY.22, CDL.26
9 PLIP interactions:9 interactions with chain K- Hydrophobic interactions: K:V.17, K:L.26, K:A.37, K:L.40, K:A.194, K:L.195, K:L.198
- Hydrogen bonds: K:S.34, K:D.229
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.8: 10 residues within 4Å:- Chain B: Q.85, D.86, L.88, S.89
- Chain K: F.74
- Chain Q: E.288, L.292
- Chain T: G.52, R.57
- Ligands: PTY.9
9 PLIP interactions:6 interactions with chain B, 3 interactions with chain T- Hydrophobic interactions: B:Q.85, B:L.88
- Hydrogen bonds: B:Q.85, B:D.86, B:D.86, B:S.89, T:G.52, T:R.57, T:R.57
LMT.17: 11 residues within 4Å:- Chain G: E.288, L.292
- Chain J: L.49, I.50, G.52, V.53, R.57
- Chain L: Q.85, D.86, S.89
- Ligands: PTY.25
8 PLIP interactions:6 interactions with chain J, 2 interactions with chain L- Hydrophobic interactions: J:L.49, J:I.50, J:V.53
- Hydrogen bonds: J:G.52, J:R.57, J:R.57, L:Q.85, L:D.86
- 2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)
XP4.12: 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.10, CDL.11
8 PLIP interactions:2 interactions with chain E, 6 interactions with chain J- Hydrogen bonds: E:S.376
- Salt bridges: E:R.372
- Hydrophobic interactions: J:F.23, J:W.31, J:F.35, J:W.38, J:W.38, J:W.38
XP4.28: 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.26, CDL.27
9 PLIP interactions:3 interactions with chain O, 6 interactions with chain T- Hydrophobic interactions: O:R.473, T:W.31, T:F.35, 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.13: 23 residues within 4Å:- Chain B: H.190
- 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, L.218, F.241, I.246, G.247, M.248, T.251, V.274, L.278
23 PLIP interactions:22 interactions with chain G, 1 interactions with chain B,- Hydrophobic interactions: G:V.119, G:V.123, G:N.192, G:A.195, G:P.197, G:P.197, G:P.198, G:L.200, G:I.203, 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, B:H.190
- Metal complexes: G:H.128
HEC.29: 23 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, 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:P.198, Q:L.200, Q:I.203, 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 3.70 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)
- 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)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(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.