SMTL ID : 6klv.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: 9 residues within 4Å: Chain A: C.111, H.113, L.114, G.115, C.116, C.135, H.138, G.139, 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: 7 residues within 4Å: Chain D: C.111, H.113, L.114, G.115, 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 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.2: 17 residues within 4Å: Chain A: G.23, A.24, Y.26, A.27, L.28, R.30 Chain B: I.53, P.82, F.83, W.85, F.87, M.259, F.266 Chain C: E.204, K.207, M.211, Y.218 12 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: A:A.24, A:Y.26, A:Y.26, A:L.28, B:P.82, B:F.83, B:F.83, B:F.87, B:F.266 Hydrogen bonds: A:R.30, C:K.207 pi-Cation interactions: C:K.207 DLX.6: 12 residues within 4Å: Chain B: Q.24, L.45, I.52, M.56, L.211, G.215, L.218, R.222 Chain E: L.208, I.209 Ligands: AMY.5, PGV.8 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:L.45, B:I.52, B:L.218, E:L.208, E:I.209 Hydrogen bonds: B:R.222 DLX.11: 17 residues within 4Å: Chain D: G.23, A.24, Y.26, A.27, L.28, R.30 Chain E: I.53, P.82, F.83, W.85, F.87, M.259, F.266 Chain F: E.204, K.207, M.211, Y.218 12 PLIP interactions: 5 interactions with chain D, 5 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: D:A.24, D:Y.26, D:Y.26, D:L.28, E:P.82, E:F.83, E:F.83, E:F.87, E:F.266 Hydrogen bonds: D:R.30, F:K.207 pi-Cation interactions: F:K.207 DLX.15: 11 residues within 4Å: Chain B: L.208, I.209, A.212 Chain E: Q.24, L.45, M.56, L.211, L.218, R.222 Ligands: PGV.8, AMY.14 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:L.208, B:I.209, B:A.212, E:L.45, E:L.218 Hydrogen bonds: E:R.222

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

HEM.3: 20 residues within 4Å: Chain B: F.48, Q.51, G.55, L.58, I.59, A.73, R.88, H.91, A.95, F.98, T.136, A.137, G.140, Y.141, L.143, P.144, H.202, V.203, P.207 Chain E: L.204 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain E, Hydrophobic interactions: B:F.48, B:Q.51, B:L.58, B:L.58, B:I.59, B:A.95, B:F.98, B:T.136, B:A.137, B:L.143, B:L.143, B:V.203, B:V.203, B:P.207, E:L.204 Salt bridges: B:R.88, B:R.88 pi-Stacking: B:H.202 Metal complexes: B:H.91 HEM.4: 23 residues within 4Å: Chain B: Y.38, G.41, I.42, A.44, 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, I.226, S.227 Ligands: AMY.5 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:L.45, B:F.98, B:V.102, B:M.106, B:W.123, B:W.123, B:I.129, B:Y.130, B:V.214, B:L.218, B:V.221, B:V.221, B:I.226 Hydrogen bonds: B:Y.38, B:Y.38, B:G.41, B:S.227 Salt bridges: B:H.105, B:R.119 Metal complexes: B:H.105 HEM.12: 20 residues within 4Å: Chain B: L.204 Chain E: F.48, Q.51, G.55, L.58, I.59, A.73, R.88, H.91, A.95, F.98, T.136, A.137, G.140, Y.141, L.143, P.144, H.202, V.203, P.207 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain B, Hydrophobic interactions: E:F.48, E:Q.51, E:L.58, E:L.58, E:I.59, E:A.95, E:F.98, E:T.136, E:A.137, E:L.143, E:L.143, E:V.203, E:V.203, E:P.207, B:L.204 Salt bridges: E:R.88, E:R.88 pi-Stacking: E:H.202 Metal complexes: E:H.91 HEM.13: 23 residues within 4Å: Chain E: Y.38, G.41, I.42, A.44, 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, I.226, S.227 Ligands: AMY.14 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:L.45, E:F.98, E:V.102, E:M.106, E:W.123, E:W.123, E:I.129, E:Y.130, E:V.214, E:L.218, E:V.221, E:V.221, E:I.226 Hydrogen bonds: E:Y.38, E:Y.38, E:G.41, E:S.227 Salt bridges: E:H.105, E:R.119 Metal complexes: E:H.105

2 x AMY: ANTIMYCIN(Non-covalent)

AMY.5: 14 residues within 4Å: Chain B: Y.28, V.30, L.34, Y.38, I.42, L.45, L.218, R.222, I.226, F.246, M.250, E.254 Ligands: HEM.4, DLX.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.30, B:L.34, B:I.226, B:F.246 Hydrogen bonds: B:Y.28, B:Y.38, B:E.254 Salt bridges: B:R.222 AMY.14: 14 residues within 4Å: Chain E: Y.28, V.30, L.34, Y.38, I.42, L.45, L.218, R.222, I.226, F.246, M.250, E.254 Ligands: HEM.13, DLX.15 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.30, E:L.34, E:I.226, E:F.246 Hydrogen bonds: E:Y.28, E:Y.38, E:E.254 Salt bridges: E:R.222

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.7: 23 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, R.342, M.355, S.358, M.359, T.362 Chain C: G.5, K.8, T.9, F.12, A.13, T.16, L.17, F.19 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.36, B:F.36, B:F.40, B:Y.103, B:Y.103, B:F.107, B:F.107, B:F.107, B:F.107, B:V.264, C:F.12, C:F.19 Hydrogen bonds: B:T.108, B:Y.112, C:T.9 Salt bridges: B:R.342, C:K.8 PGV.8: 6 residues within 4Å: Chain B: I.20, Q.24 Chain E: I.20, Q.24 Ligands: DLX.6, DLX.15 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.16: 22 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, R.342, M.355, S.358, M.359, T.362 Chain F: K.8, T.9, F.12, A.13, T.16, L.17, F.19 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:F.36, E:F.36, E:F.40, E:Y.103, E:Y.103, E:F.107, E:F.107, E:F.107, E:F.107, E:V.264, F:F.12, F:F.19 Hydrogen bonds: E:T.108, E:Y.112, F:T.9 Salt bridges: E:R.342, F:K.8

2 x HEC: HEME C(Covalent)

HEC.9: 20 residues within 4Å: Chain C: C.70, C.73, H.74, L.136, Q.138, P.141, L.143, M.146, R.150, Y.154, L.155, F.158, I.159, L.166, T.169, M.171, P.172, L.174, I.190 Chain D: H.138 19 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: C:L.136, C:Q.138, C:Q.138, C:L.143, C:L.155, C:F.158, C:F.158, C:I.159, C:M.171, C:P.172, C:L.174, C:L.174, C:I.190, C:I.190 Hydrogen bonds: C:Y.154 Salt bridges: C:R.150, D:H.138, B:K.289 Metal complexes: C:H.74 HEC.17: 20 residues within 4Å: Chain A: H.138 Chain F: C.70, C.73, H.74, L.136, Q.138, P.141, L.143, M.146, R.150, Y.154, L.155, F.158, I.159, L.166, T.169, M.171, P.172, L.174, I.190 19 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 17 interactions with chain F, Salt bridges: A:H.138, E:K.289, F:R.150 Hydrophobic interactions: F:L.136, F:Q.138, F:Q.138, F:L.143, F:L.155, F:F.158, F:F.158, F:I.159, F:M.171, F:P.172, F:L.174, F:L.174, F:I.190, 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: 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

Cytochrome c

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