SMTL ID : 6kls.1

Hyperthermophilic respiratory Complex III

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: C.111, H.113, L.114, G.115, C.116, C.135, H.138, G.140 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.111, A:H.113, A:C.135, A:H.138 FES.10: 6 residues within 4Å: Chain D: C.111, H.113, L.114, C.116, C.135, H.138 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.111, D:H.113, D:C.135, D:H.138

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

HEM.2: 24 residues within 4Å: Chain B: F.48, Q.51, I.52, G.55, M.56, L.58, I.59, A.73, R.88, H.91, A.92, A.95, F.98, T.136, A.137, G.140, Y.141, L.143, P.144, H.202, V.203, P.207, L.210 Chain E: L.204 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain E, Hydrophobic interactions: B:F.48, B:I.52, B:L.58, B:I.59, B:A.95, B:F.98, B:T.136, B:A.137, B:L.143, B:V.203, B:P.207, B:L.210, E:L.204 Salt bridges: B:R.88, B:R.88 Metal complexes: B:H.202 HEM.3: 22 residues within 4Å: Chain B: Y.38, G.41, I.42, L.45, F.98, V.102, H.105, M.106, A.114, R.119, W.123, G.126, W.127, I.129, Y.130, V.214, H.217, L.218, V.221, G.225, S.227 Ligands: DLX.4 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:I.42, B:L.45, B:F.98, B:V.102, B:M.106, B:A.114, B:W.123, B:W.123, B:I.129, B:Y.130, B:V.214, B:V.214, B:L.218, B:V.221, B:V.221 Hydrogen bonds: B:Y.38, B:G.41, B:S.227 Salt bridges: B:H.105, B:R.119 Metal complexes: B:H.105 HEM.11: 24 residues within 4Å: Chain B: L.204 Chain E: F.48, Q.51, I.52, G.55, M.56, L.58, I.59, A.73, R.88, H.91, A.92, A.95, F.98, T.136, A.137, G.140, Y.141, L.143, P.144, H.202, V.203, P.207, L.210 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain B, Hydrophobic interactions: E:F.48, E:I.52, E:L.58, E:I.59, E:A.95, E:F.98, E:T.136, E:A.137, E:L.143, E:V.203, E:P.207, E:L.210, B:L.204 Salt bridges: E:R.88, E:R.88 Metal complexes: E:H.202 HEM.12: 22 residues within 4Å: Chain E: Y.38, G.41, I.42, L.45, F.98, V.102, H.105, M.106, A.114, R.119, W.123, G.126, W.127, I.129, Y.130, V.214, H.217, L.218, V.221, G.225, S.227 Ligands: DLX.13 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:L.45, E:F.98, E:V.102, E:M.106, E:A.114, E:W.123, E:W.123, E:I.129, E:Y.130, E:V.214, E:V.214, E:L.218, E:V.221, E:V.221 Hydrogen bonds: E:Y.38, E:G.41, E:S.227 Salt bridges: E:H.105, E:R.119 Metal complexes: E:H.105

6 x DLX: 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15,19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione(Non-covalent)

DLX.4: 11 residues within 4Å: Chain B: L.218, V.221, R.222 Chain E: F.131, W.183, I.209, L.213, I.216 Ligands: HEM.3, DLX.5, PGV.7 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:F.131, E:I.209, E:L.213, E:L.213, E:I.216, B:V.221, B:R.222 DLX.5: 13 residues within 4Å: Chain B: Q.24, L.45, F.48, A.49, M.56, L.211, L.218, R.222 Chain E: L.208, I.209, A.212 Ligands: DLX.4, PGV.7 9 PLIP interactions: 2 interactions with chain E, 7 interactions with chain B Hydrophobic interactions: E:L.208, E:A.212, B:F.48, B:A.49, B:L.211, B:L.218 Hydrogen bonds: B:Q.24, B:Q.24, B:R.222 DLX.8: 19 residues within 4Å: Chain A: G.17, G.23, A.24, Y.26, A.27, R.30 Chain B: I.53, P.82, F.83, W.85, L.86, F.87, I.90, M.259, F.266 Chain C: E.204, K.207, M.211, V.215 15 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:Y.26, A:A.27, B:P.82, B:F.83, B:L.86, B:F.87, B:F.87, B:I.90, B:F.266, C:V.215 Hydrogen bonds: A:Y.26, A:R.30 pi-Stacking: B:F.83, B:F.83 pi-Cation interactions: C:K.207 DLX.13: 11 residues within 4Å: Chain B: F.131, W.183, I.209, L.213, I.216 Chain E: L.218, V.221, R.222 Ligands: PGV.7, HEM.12, DLX.14 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain B Hydrophobic interactions: E:V.221, E:R.222, B:F.131, B:I.209, B:L.213, B:L.213, B:I.216 DLX.14: 13 residues within 4Å: Chain B: L.208, I.209, A.212 Chain E: Q.24, L.45, F.48, A.49, M.56, L.211, L.218, R.222 Ligands: PGV.7, DLX.13 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:F.48, E:A.49, E:L.211, E:L.218, B:L.208, B:A.212 Hydrogen bonds: E:Q.24, E:Q.24, E:R.222 DLX.16: 19 residues within 4Å: Chain D: G.17, G.23, A.24, Y.26, A.27, R.30 Chain E: I.53, P.82, F.83, W.85, L.86, F.87, I.90, M.259, F.266 Chain F: E.204, K.207, M.211, V.215 15 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F, 4 interactions with chain D Hydrophobic interactions: E:P.82, E:F.83, E:L.86, E:F.87, E:F.87, E:I.90, E:F.266, F:V.215, D:Y.26, D:A.27 pi-Stacking: E:F.83, E:F.83 pi-Cation interactions: F:K.207 Hydrogen bonds: D:Y.26, D:R.30

3 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Covalent)(Non-covalent)

PGV.6: 25 residues within 4Å: Chain B: F.36, P.37, F.40, Y.103, L.104, F.107, T.108, Y.111, Y.112, V.264, F.267, Y.303, R.342, F.351, M.355, S.358, M.359, T.362 Chain C: G.5, K.8, T.9, F.12, T.16, L.17, F.19 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.36, B:F.40, B:Y.103, B:F.107, B:F.107, B:F.107, B:F.107, B:T.108, B:V.264, B:F.267, B:Y.303, C:L.17, C:F.19 Hydrogen bonds: B:Y.112 Salt bridges: B:R.342, C:K.8 PGV.7: 10 residues within 4Å: Chain B: I.20, Q.24, A.212 Chain E: I.20, Q.24, A.212 Ligands: DLX.4, DLX.5, DLX.13, DLX.14 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:I.20, B:I.20 Hydrogen bonds: E:Q.24, B:Q.24 PGV.15: 25 residues within 4Å: Chain E: F.36, P.37, F.40, Y.103, L.104, F.107, T.108, Y.111, Y.112, V.264, F.267, Y.303, R.342, F.351, M.355, S.358, M.359, T.362 Chain F: G.5, K.8, T.9, F.12, T.16, L.17, F.19 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:F.36, E:F.40, E:Y.103, E:F.107, E:F.107, E:F.107, E:F.107, E:T.108, E:V.264, E:F.267, E:Y.303, F:L.17, F:F.19 Hydrogen bonds: E:Y.112 Salt bridges: E:R.342, F:K.8

2 x HEC: HEME C(Covalent)

HEC.9: 23 residues within 4Å: Chain B: K.289 Chain C: C.70, C.73, H.74, L.136, Q.138, P.140, L.143, M.146, R.150, Y.154, L.155, F.158, I.159, L.166, T.169, T.170, M.171, P.172, L.174, I.190 Chain D: L.114, H.138 18 PLIP interactions: 15 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: C:Q.138, C:P.140, C:L.143, C:L.155, C:F.158, C:I.159, C:T.169, C:M.171, C:P.172, C:L.174, C:L.174, C:I.190 Hydrogen bonds: C:Y.154 Salt bridges: C:R.150, B:K.289, B:K.289, D:H.138 Metal complexes: C:H.74 HEC.17: 23 residues within 4Å: Chain A: L.114, H.138 Chain E: K.289 Chain F: C.70, C.73, H.74, L.136, Q.138, P.140, L.143, M.146, R.150, Y.154, L.155, F.158, I.159, L.166, T.169, T.170, M.171, P.172, L.174, I.190 18 PLIP interactions: 1 interactions with chain A, 15 interactions with chain F, 2 interactions with chain E, Salt bridges: A:H.138, F:R.150, E:K.289, E:K.289 Hydrophobic interactions: F:Q.138, F:P.140, F:L.143, F:L.155, F:F.158, F:I.159, F:T.169, F:M.171, F:P.172, F:L.174, F:L.174, F:I.190 Hydrogen bonds: F:Y.154 Metal complexes: F:H.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, G. et al., A 3.3 angstrom -Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-05-13

Peptides

Rieske-I iron sulfur protein: AD
cytochrome b subunit: BE
Cytochrome c: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
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Rieske-I iron sulfur protein

cytochrome b subunit

Cytochrome c

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