- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.10 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 6 x HEC: HEME C(Non-covalent)
- 4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PC1.3: 10 residues within 4Å:- Chain A: F.29, Y.94, Y.102, Y.103, A.317, G.327, I.330
- Chain H: Q.53, V.57
- Ligands: CDL.15
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:F.29, A:Y.102, A:Y.102, A:I.330, A:I.330
- Hydrogen bonds: A:Y.103
- Salt bridges: A:K.323
PC1.16: 14 residues within 4Å:- Chain E: D.445, M.472
- Chain I: Y.8, V.12, K.13, N.15, F.18, I.22
- Chain L: Y.66, G.73, S.76, A.77
- Ligands: PTY.4, CDL.10
4 PLIP interactions:2 interactions with chain I, 1 interactions with chain E, 1 interactions with chain L- Hydrophobic interactions: I:I.22, L:A.77
- Hydrogen bonds: I:N.15
- Salt bridges: E:D.445
PC1.19: 11 residues within 4Å:- Chain K: F.29, Y.94, Y.102, Y.103, A.317, G.327, I.330
- Chain R: Q.53, F.56, V.57
- Ligands: CDL.20
8 PLIP interactions:8 interactions with chain K- Hydrophobic interactions: K:F.29, K:F.29, K:Y.102, K:Y.102, K:I.330, K:I.330
- Hydrogen bonds: K:Y.103
- Salt bridges: K:K.323
PC1.30: 17 residues within 4Å:- Chain B: Y.66, I.69, G.73, S.76, A.77
- Chain O: D.445, M.472
- Chain S: Y.8, V.12, K.13, N.15, F.18, V.19, I.22, L.23
- Ligands: PTY.21, CDL.25
6 PLIP interactions:5 interactions with chain S, 1 interactions with chain O- Hydrophobic interactions: S:V.19, S:I.22, S:I.22, S:L.23
- Hydrogen bonds: S:N.15
- Salt bridges: O:D.445
- 4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)
PTY.4: 17 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: CDL.10, PC1.16
12 PLIP interactions:2 interactions with chain G, 8 interactions with chain A, 2 interactions with chain L- Salt bridges: G:K.314, G:K.314, A:H.222, A:H.222
- 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
PTY.9: 19 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.240, F.245
- Chain Q: L.292, K.295, A.296, V.299, I.300
- Chain S: D.30
- Ligands: LMT.31
6 PLIP interactions:1 interactions with chain Q, 3 interactions with chain K, 1 interactions with chain S, 1 interactions with chain B- Salt bridges: Q:K.295
- Hydrophobic interactions: K:F.77, K:L.237, K:F.240, B:V.84
- Hydrogen bonds: S:D.30
PTY.21: 16 residues within 4Å:- Chain B: 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: CDL.25, PC1.30
11 PLIP interactions:6 interactions with chain K, 2 interactions with chain B, 2 interactions with chain Q, 1 interactions with chain O- Hydrophobic interactions: K:A.37, K:F.227, K:D.229, K:L.230, B:F.72, B:F.72
- Salt bridges: K:H.222, K:H.222, Q:K.314, Q:K.314
- Hydrogen bonds: O:N.467
PTY.24: 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.23
9 PLIP interactions:4 interactions with chain L, 2 interactions with chain A, 2 interactions with chain G, 1 interactions with chain I- Hydrophobic interactions: L:A.80, L:V.84, A:F.77, A:L.237, G:I.300
- Hydrogen bonds: L:K.81, L:D.86, I:D.30
- Salt bridges: G:K.295
- 10 x CDL: CARDIOLIPIN(Non-covalent)
CDL.5: 12 residues within 4Å:- Chain A: T.108, P.109, R.110, V.111, L.112, S.115, L.303, I.307
- Chain K: L.3, K.6, N.7, L.10
8 PLIP interactions:6 interactions with chain A, 2 interactions with chain K- Hydrophobic interactions: A:V.111, 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.7: 11 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
8 PLIP interactions:6 interactions with chain K, 2 interactions with chain A- Hydrophobic interactions: K:V.111
- Hydrogen bonds: K:T.108, K:P.109, K:P.109, K:V.111, K:L.112, A:N.7
- Salt bridges: A:K.6
CDL.10: 13 residues within 4Å:- Chain A: R.4, H.222
- Chain E: H.364, K.368, M.471, M.472, R.473
- Chain I: N.15
- Chain J: W.38
- Ligands: PTY.4, CDL.11, XP4.12, PC1.16
10 PLIP interactions:7 interactions with chain E, 1 interactions with chain J, 2 interactions with chain A- 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
- Hydrophobic interactions: J:W.38
CDL.11: 7 residues within 4Å:- Chain A: 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: 16 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, A.54, V.57
- Ligands: PC1.3, CDL.14
13 PLIP interactions:1 interactions with chain C, 6 interactions with chain H, 6 interactions with chain A- Salt bridges: C:H.84, H:R.49, H:R.49, H:R.49
- Hydrophobic interactions: H:T.50, H:V.57, A:Y.28, A:F.32, A:L.35, A:T.232
- Hydrogen bonds: H:Q.53, A:N.27, A:Y.28
CDL.20: 17 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: T.46, R.49, T.50, Q.53, A.54, V.57
- Ligands: PC1.19, CDL.29
12 PLIP interactions:6 interactions with chain K, 5 interactions with chain R, 1 interactions with chain M- Hydrophobic interactions: K:Y.28, K:F.32, K:L.35, K:T.232, R:T.46, R:V.57
- Hydrogen bonds: K:Y.28, K:Y.103
- Salt bridges: R:R.49, R:R.49, R:R.49, M:H.84
CDL.25: 14 residues within 4Å:- Chain K: R.4, H.222, S.226
- Chain O: H.364, K.368, M.471, M.472, R.473
- Chain S: N.15
- Chain T: W.38
- Ligands: PTY.21, CDL.26, XP4.27, PC1.30
10 PLIP interactions:8 interactions with chain O, 2 interactions with chain K- Hydrophobic interactions: O:M.472
- 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.26: 8 residues within 4Å:- Chain K: A.2, L.3
- Chain O: H.364, F.365, R.372, R.473
- Ligands: CDL.25, XP4.27
5 PLIP interactions:1 interactions with chain K, 4 interactions with chain O- Hydrogen bonds: K:L.3
- Salt bridges: O:H.364, O:R.372, O:R.473, O:R.473
CDL.29: 12 residues within 4Å:- Chain K: Y.28
- Chain M: H.84
- Chain Q: V.308, K.311, K.312
- Chain R: V.38, A.41, A.42, N.45, T.46, R.49
- Ligands: CDL.20
8 PLIP interactions:3 interactions with chain Q, 5 interactions with chain R- Salt bridges: Q:K.311, Q:K.312, Q:K.319, R:R.49
- Hydrophobic interactions: R:V.38
- Hydrogen bonds: R:N.45, R:R.49, R:R.49
- 4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.6: 12 residues within 4Å:- Chain A: N.11, M.12, A.13, S.15, Y.16, V.17, L.195, I.199, H.202
- Chain H: W.10
- Chain K: M.12
- Ligands: LMT.22
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:M.12, A:Y.16, A:Y.16, A:Y.16, A:V.17, A:L.195, A:I.199
- Hydrogen bonds: A:N.11, A:N.11, A:N.14, A:S.15, A:Y.16
LMT.22: 10 residues within 4Å:- Chain A: M.12
- Chain K: N.11, M.12, S.15, Y.16, V.17, L.195, H.202
- Chain R: W.10
- Ligands: LMT.6
9 PLIP interactions:9 interactions with chain K- Hydrophobic interactions: K:M.12, K:Y.16, K:V.17, K:L.195
- Hydrogen bonds: K:N.11, K:N.11, K:N.14, K:S.15, K:Y.16
LMT.23: 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.24
11 PLIP interactions:7 interactions with chain J, 4 interactions with chain L- Hydrophobic interactions: J:L.49, J:L.49, J:I.50, J:V.53, L:Q.85
- Hydrogen bonds: J:G.52, J:R.57, J:R.57, L:Q.85, L:D.86, L:S.89
LMT.31: 9 residues within 4Å:- Chain B: Q.85, D.86, L.88, S.89
- Chain Q: E.288, L.292
- Chain T: G.52, R.57
- Ligands: PTY.9
10 PLIP interactions:3 interactions with chain T, 7 interactions with chain B- Hydrogen bonds: T:G.52, T:R.57, T:R.57, B:Q.85, B:D.86, B:D.86, B:S.89
- Hydrophobic interactions: B:Q.85, B:L.88, B:L.88
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 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
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
XP4.27: 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.25, CDL.26
7 PLIP interactions:5 interactions with chain T, 2 interactions with chain O- Hydrophobic interactions: 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
- 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 3.10 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 6 x HEC: HEME C(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)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 2 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(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.