SMTL ID : 6lum.1

Structure of Mycobacterium smegmatis succinate dehydrogenase 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.84 Å

Oligo State

hetero-3-3-3-3-3-mer

Ligands

6 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.1: 8 residues within 4Å: Chain A: L.96, F.99, W.100, A.101 Chain B: I.56, F.60 Chain E: R.255 Ligands: CDL.34 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:L.96, A:F.99, B:I.56, B:F.60 Hydrogen bonds: A:A.101 Salt bridges: E:R.255 PEV.2: 15 residues within 4Å: Chain A: L.32, T.36, F.43, V.73, L.75, M.76, G.79, L.80, F.86, F.118, L.119, F.122 Chain C: L.9, V.13, I.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.32, A:T.36, A:F.86, A:F.118, A:L.119, A:F.122 PEV.14: 12 residues within 4Å: Chain F: F.43, V.73, L.75, M.76, G.79, L.80, F.86, F.118, L.119, F.122 Chain H: V.13, I.16 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.75, F:F.86, F:F.118, F:L.119, F:F.122 PEV.25: 8 residues within 4Å: Chain F: I.92, L.96, F.99, W.100, A.101, L.117 Chain J: R.255 Ligands: CDL.6 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain J Hydrophobic interactions: F:I.92, F:L.96, F:L.117 Hydrogen bonds: F:A.101 Salt bridges: J:R.255 PEV.28: 16 residues within 4Å: Chain K: F.43, Y.68, V.73, L.75, M.76, G.79, L.80, A.82, F.86, A.115, F.118, L.119, F.122 Chain M: L.9, V.13, I.16 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:L.75, K:A.82, K:F.86, K:A.115, K:F.118, K:L.119, K:F.122 PEV.39: 8 residues within 4Å: Chain G: V.124, W.128 Chain K: I.95, F.99, W.100 Chain O: R.255, F.259 Ligands: CDL.19 3 PLIP interactions: 1 interactions with chain O, 1 interactions with chain K, 1 interactions with chain G Salt bridges: O:R.255 Hydrophobic interactions: K:F.99, G:W.128

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

HEM.3: 23 residues within 4Å: Chain A: W.30, H.33, R.34, G.37, A.38, I.40, L.44, H.87, A.88, G.91, I.95 Chain B: M.51, R.52, G.55, L.58, V.59, A.104, H.107, G.108, G.111, T.114 Chain E: R.231 Ligands: HEM.4 12 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A, 2 interactions with chain E, Hydrophobic interactions: B:L.58, B:V.59, A:I.40, A:L.44, A:A.88, A:I.95 Salt bridges: B:R.52, A:R.34, E:R.231, E:R.231 Metal complexes: B:H.107 pi-Stacking: A:H.33 HEM.4: 23 residues within 4Å: Chain A: I.40, F.43, L.44, H.47, T.51, E.77, L.80, V.84 Chain B: H.65, L.66, M.69, L.70, V.76, I.79, V.84, R.87, W.88, D.97, L.100, L.101, G.144, L.148 Ligands: HEM.3 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A, Hydrophobic interactions: B:L.70, B:V.76, B:I.79, B:V.84, B:L.100, B:L.100, B:L.101, A:I.40, A:F.43, A:L.44, A:T.51, A:E.77, A:L.80, A:V.84 Salt bridges: B:R.87 pi-Stacking: B:H.65 Metal complexes: A:H.47 HEM.16: 23 residues within 4Å: Chain F: I.40, F.43, L.44, H.47, T.51, Y.61, E.77, L.80 Chain G: H.65, L.66, M.69, L.70, V.76, I.79, V.84, R.87, W.88, D.97, L.100, L.101, G.144, L.148 Ligands: HEM.17 15 PLIP interactions: 8 interactions with chain G, 7 interactions with chain F, Hydrophobic interactions: G:L.70, G:V.76, G:I.79, G:V.84, G:L.100, G:L.100, G:L.101, F:I.40, F:F.43, F:L.44, F:T.51, F:E.77, F:L.80 Salt bridges: G:R.87 Metal complexes: F:H.47 HEM.17: 24 residues within 4Å: Chain F: W.30, H.33, R.34, G.37, A.38, I.40, F.41, H.87, A.88, G.91, I.92, I.95 Chain G: M.51, R.52, G.55, L.58, V.59, A.104, H.107, G.108, G.111, T.114 Chain J: R.231 Ligands: HEM.16 13 PLIP interactions: 6 interactions with chain F, 2 interactions with chain J, 5 interactions with chain G, Hydrophobic interactions: F:I.40, F:A.88, F:I.95, F:I.95, G:L.58, G:V.59, G:A.104 Salt bridges: F:R.34, J:R.231, J:R.231, G:R.52 pi-Stacking: F:H.33 Metal complexes: G:H.107 HEM.26: 22 residues within 4Å: Chain K: W.30, H.33, R.34, G.37, A.38, I.40, L.44, H.87, A.88, G.91 Chain L: M.51, R.52, G.55, L.58, V.59, A.104, H.107, G.108, G.111, T.114 Chain O: R.231 Ligands: HEM.30 11 PLIP interactions: 5 interactions with chain K, 4 interactions with chain L, 2 interactions with chain O, Hydrophobic interactions: K:I.40, K:L.44, K:A.88, L:L.58, L:V.59 Salt bridges: K:R.34, L:R.52, O:R.231, O:R.231 pi-Stacking: K:H.33 Metal complexes: L:H.107 HEM.30: 24 residues within 4Å: Chain K: I.40, F.43, L.44, H.47, T.51, Y.61, Y.68, E.77, L.80 Chain L: H.65, L.66, M.69, L.70, V.76, I.79, V.84, R.87, W.88, D.97, L.100, L.101, G.144, L.148 Ligands: HEM.26 16 PLIP interactions: 8 interactions with chain K, 8 interactions with chain L, Hydrophobic interactions: K:I.40, K:F.43, K:L.44, K:T.51, K:Y.68, K:E.77, K:L.80, L:L.70, L:V.76, L:I.79, L:V.84, L:L.100, L:L.100, L:L.101 Metal complexes: K:H.47 Salt bridges: L:R.87

6 x MQ9: MENAQUINONE-9(Non-covalent)

MQ9.5: 5 residues within 4Å: Chain B: G.64, F.67, I.68, W.72, Q.73 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.68 MQ9.7: 12 residues within 4Å: Chain B: V.142, S.145, Y.146, V.149, T.150 Chain G: Q.94, I.95, M.98, A.99, W.102, V.149 Ligands: LPP.15 9 PLIP interactions: 5 interactions with chain G, 4 interactions with chain B Hydrophobic interactions: G:M.98, G:A.99, G:W.102, G:V.149, B:V.142, B:T.150 Hydrogen bonds: G:Q.94 pi-Stacking: B:Y.146, B:Y.146 MQ9.18: 4 residues within 4Å: Chain G: G.64, F.67, I.68, W.72 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.68, G:W.72 MQ9.29: 10 residues within 4Å: Chain B: Q.94, M.98, W.102, L.148, V.149 Chain L: V.142, S.145, Y.146, V.149, T.150 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain L Hydrophobic interactions: B:Q.94, B:M.98, B:W.102, B:V.149 Hydrogen bonds: L:T.150 pi-Stacking: L:Y.146, L:Y.146 MQ9.31: 6 residues within 4Å: Chain L: F.67, I.68, W.72, Q.73, F.92, W.93 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.67, L:I.68, L:W.93 MQ9.32: 11 residues within 4Å: Chain G: V.142, S.145, Y.146, V.149, T.150 Chain L: Q.94, I.95, M.98, W.102, V.149 Ligands: LPP.33 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain L Hydrophobic interactions: G:V.142, L:M.98, L:W.102, L:V.149 pi-Stacking: G:Y.146, G:Y.146 Hydrogen bonds: L:Q.94

3 x CDL: CARDIOLIPIN(Covalent)

CDL.6: 21 residues within 4Å: Chain A: F.42, F.45 Chain B: M.112, I.116, Y.119, A.120, R.121, K.122, V.124, T.125, W.128, L.129, L.133, L.135, A.136 Chain C: V.15, W.18, Y.22 Chain G: F.53 Ligands: PIE.9, PEV.25 16 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B, 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: A:F.42, A:F.45, B:I.116, B:I.116, B:W.128, B:W.128, B:L.129, B:A.136, C:V.15, C:W.18, G:F.53 Hydrogen bonds: B:R.121, B:K.122 Salt bridges: B:R.121, B:K.122, B:K.122 CDL.19: 20 residues within 4Å: Chain F: F.42, F.45, V.46 Chain G: M.112, I.116, Y.119, A.120, R.121, K.122, V.124, T.125, W.128, L.129, L.133, L.135, A.136 Chain H: W.18, Y.22 Ligands: PIE.20, PEV.39 15 PLIP interactions: 12 interactions with chain G, 1 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: G:I.116, G:W.128, G:W.128, G:W.128, G:L.129, G:L.133, G:L.135, G:A.136, H:W.18, F:F.42, F:V.46 Hydrogen bonds: G:R.121, G:K.122 Salt bridges: G:R.121, G:K.122 CDL.34: 18 residues within 4Å: Chain K: F.42 Chain L: M.112, I.116, Y.119, A.120, R.121, K.122, V.124, T.125, W.128, L.129, L.133, L.135, A.136 Chain M: W.18, Y.22 Ligands: PEV.1, PIE.27 14 PLIP interactions: 1 interactions with chain K, 12 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: K:F.42, L:I.116, L:W.128, L:W.128, L:W.128, L:L.129, L:L.133, L:L.135, L:A.136, M:W.18 Hydrogen bonds: L:R.121, L:K.122 Salt bridges: L:R.121, L:K.122

3 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)

LPP.8: 6 residues within 4Å: Chain B: F.92, I.95, A.99 Chain K: L.53, V.56 Chain M: F.4 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: B:F.92, B:I.95, B:A.99, M:F.4, K:L.53 LPP.15: 4 residues within 4Å: Chain A: L.53 Chain G: S.90, F.92 Ligands: MQ9.7 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain A Hydrophobic interactions: G:F.92, A:L.53 Hydrogen bonds: G:S.90 LPP.33: 7 residues within 4Å: Chain F: L.53 Chain H: F.4 Chain L: S.90, F.92, W.93, I.95 Ligands: MQ9.32 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain H Hydrophobic interactions: L:F.92, L:I.95, L:I.95, H:F.4 Hydrogen bonds: L:S.90

3 x PIE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL(Non-covalent)(Covalent)

PIE.9: 8 residues within 4Å: Chain B: R.121 Chain C: L.14, T.17, W.18, V.21, Y.22, Y.25 Ligands: CDL.6 9 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:T.17, C:W.18, C:W.18, C:W.18 Hydrogen bonds: C:Y.22, C:Y.25, A:R.16, B:R.121, B:R.121 PIE.20: 11 residues within 4Å: Chain F: R.16 Chain G: R.121 Chain H: A.11, L.14, V.15, T.17, W.18, V.21, Y.22, Y.25 Ligands: CDL.19 14 PLIP interactions: 10 interactions with chain H, 2 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: H:A.11, H:L.14, H:T.17, H:W.18, H:W.18, H:W.18, H:V.21 Hydrogen bonds: H:Y.22, H:Y.22, H:Y.25, F:R.16, F:R.16, G:R.121, G:R.121 PIE.27: 9 residues within 4Å: Chain K: R.16 Chain L: R.121 Chain M: L.14, T.17, W.18, V.21, Y.22, Y.25 Ligands: CDL.34 9 PLIP interactions: 7 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:L.14, M:T.17, M:W.18, M:W.18 Hydrogen bonds: M:Y.22, M:Y.22, M:Y.25, L:R.121, L:R.121

3 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.10: 34 residues within 4Å: Chain D: V.12, G.13, A.14, G.15, G.16, A.17, L.34, T.35, K.36, L.37, S.42, H.43, T.44, A.46, A.47, Q.48, G.49, F.162, A.164, A.202, T.203, G.204, S.214, N.215, D.222, H.354, Y.355, G.383, E.384, R.395, T.398, N.399, S.400, L.401 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:A.14, D:G.16, D:A.17, D:K.36, D:L.37, D:S.42, D:T.44, D:T.44, D:Q.48, D:G.49, D:A.164, D:A.164, D:G.204, D:D.222, D:E.384, D:E.384, D:R.395, D:T.398, D:S.400, D:S.400, D:S.400, D:S.400, D:L.401 pi-Cation interactions: D:H.354 FAD.21: 34 residues within 4Å: Chain I: V.12, G.13, A.14, G.15, G.16, A.17, L.34, T.35, K.36, L.37, S.42, H.43, T.44, A.46, A.47, G.49, F.162, A.164, A.202, T.203, G.204, S.214, D.222, L.253, H.354, Y.355, G.383, E.384, R.395, T.398, N.399, S.400, L.401, I.404 27 PLIP interactions: 27 interactions with chain I Hydrophobic interactions: I:A.46, I:L.253 Hydrogen bonds: I:A.14, I:G.16, I:A.17, I:K.36, I:L.37, I:S.42, I:T.44, I:Q.48, I:G.49, I:G.50, I:A.164, I:G.204, I:D.222, I:D.222, I:E.384, I:E.384, I:R.395, I:T.398, I:S.400, I:S.400, I:S.400, I:S.400, I:L.401 pi-Stacking: I:H.354 pi-Cation interactions: I:R.395 FAD.35: 35 residues within 4Å: Chain N: V.12, G.13, A.14, G.15, G.16, A.17, L.34, T.35, K.36, S.42, H.43, T.44, A.46, A.47, Q.48, G.49, G.50, F.162, A.164, A.202, T.203, G.204, S.214, L.219, D.222, L.253, H.354, Y.355, G.383, E.384, R.395, T.398, S.400, L.401, I.404 23 PLIP interactions: 23 interactions with chain N Hydrophobic interactions: N:L.253 Hydrogen bonds: N:A.14, N:G.16, N:A.17, N:K.36, N:L.37, N:S.42, N:H.43, N:T.44, N:Q.48, N:G.49, N:G.50, N:A.164, N:G.204, N:D.222, N:D.222, N:E.384, N:E.384, N:R.395, N:S.400, N:S.400, N:L.401 pi-Cation interactions: N:H.354

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

FES.11: 6 residues within 4Å: Chain E: S.76, C.77, C.82, G.83, D.85, C.97 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.77, E:C.82, E:D.85, E:D.85, E:C.97 FES.22: 6 residues within 4Å: Chain J: C.77, C.82, G.83, S.84, D.85, C.97 5 PLIP interactions: 5 interactions with chain J, Metal complexes: J:C.77, J:C.82, J:D.85, J:D.85, J:C.97 FES.36: 6 residues within 4Å: Chain O: C.77, C.82, G.83, S.84, D.85, C.97 5 PLIP interactions: 5 interactions with chain O, Metal complexes: O:C.77, O:C.82, O:D.85, O:D.85, O:C.97

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.12: 8 residues within 4Å: Chain E: C.174, I.175, L.176, C.177, A.178, C.180, C.240, P.241 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.174, E:C.177, E:C.180, E:C.240 SF4.23: 8 residues within 4Å: Chain J: C.174, I.175, L.176, C.177, A.178, C.180, C.240, P.241 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.174, J:C.177, J:C.180, J:C.240 SF4.37: 8 residues within 4Å: Chain O: C.174, I.175, L.176, C.177, A.178, C.180, C.240, P.241 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.174, O:C.177, O:C.180, O:C.240

3 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.13: 11 residues within 4Å: Chain E: C.184, V.186, Y.193, C.230, R.231, T.232, T.233, N.235, C.236, T.247, I.250 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.184, E:C.230, E:T.233, E:C.236 F3S.24: 12 residues within 4Å: Chain J: C.184, V.186, Y.193, P.196, C.230, R.231, T.232, T.233, N.235, C.236, T.247, I.250 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.184, J:C.230, J:T.233, J:C.236 F3S.38: 11 residues within 4Å: Chain O: C.184, V.186, P.196, C.230, R.231, T.232, T.233, N.235, C.236, T.247, I.250 4 PLIP interactions: 4 interactions with chain O, Metal complexes: O:C.184, O:C.230, O:T.233, O:C.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, H. et al., Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. Nat Commun (2020)

Release Date

2020-05-27

Peptides

Succinate dehydrogenase subunit C: AFK
Succinate dehydrogenase subunit D: BGL
Succinate dehydrogenase subunit F: CHM
Succinate dehydrogenase subunit A: DIN
Succinate dehydrogenase subunit B: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

F
G

K
M

B
D

G
H

L
N

C
E

H
I

M
O

D
A

I
J

N
P

E
B

J
K

O
Q

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase subunit C

Succinate dehydrogenase subunit D

Succinate dehydrogenase subunit F

Succinate dehydrogenase subunit A

Succinate dehydrogenase subunit B