SMTL ID : 6q9d.1

CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: P.204, S.359, C.360, G.361, Q.362, C.363, C.366, T.404, I.405, C.406, L.408 6 PLIP interactions: 6 interactions with chain A, Salt bridges: A:E.189, A:E.189 Metal complexes: A:C.360, A:C.363, A:C.366, A:C.406 SF4.4: 11 residues within 4Å: Chain C: H.101, D.104, C.105, C.108, G.111, C.114, L.116, Q.117, R.152, V.205, G.206 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.101, C:C.105, C:C.108, C:C.114 SF4.5: 9 residues within 4Å: Chain C: M.150, C.153, I.154, Q.155, C.156, T.157, C.159, C.203, V.205 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.153, C:C.156, C:C.159, C:C.203 SF4.7: 10 residues within 4Å: Chain D: R.105 Chain F: A.53, C.54, C.55, G.90, G.117, S.118, C.119, C.149, P.150 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.54, F:C.55, F:C.119, F:C.149 SF4.8: 11 residues within 4Å: Chain G: C.87, P.88, A.89, I.92, C.116, I.117, Y.118, C.119, G.120, C.122, E.133 4 PLIP interactions: 4 interactions with chain G, Salt bridges: G:E.133 Metal complexes: G:C.87, G:C.116, G:C.122 SF4.9: 12 residues within 4Å: Chain G: C.77, I.78, A.79, C.80, K.81, L.82, C.83, I.94, Y.109, C.126, A.130, I.131 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.77, G:C.80, G:C.83, G:C.126

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: G.68, R.69, G.70, G.71, A.72, G.73, F.74, K.79, N.97, D.99, Y.185, G.188, E.189, E.190, V.223, N.225, T.228, A.407 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.185, A:E.189, A:A.407 Hydrogen bonds: A:R.69, A:R.69, A:G.70, A:A.72, A:G.73, A:F.74, A:K.79, A:N.97, A:D.99 Salt bridges: A:K.79

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

FES.3: 9 residues within 4Å: Chain B: C.103, T.105, C.108, C.144, L.145, G.146, A.147, C.148, M.153 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.103, B:C.108, B:C.144, B:C.148 FES.6: 8 residues within 4Å: Chain C: C.41, Y.42, G.50, N.51, C.52, R.53, C.55, C.69 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.41, C:C.52, C:C.55, C:C.69

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain I: C.59, H.68, V.71, C.84, C.87 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.59, I:H.68, I:C.84, I:C.87

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.11: 20 residues within 4Å: Chain K: G.25, T.27, G.28, F.29, L.30, R.50, C.51, W.73, V.95, G.96, R.97, F.104, I.132, H.134, Y.145, K.149, P.168, A.169, I.171, R.177 19 PLIP interactions: 19 interactions with chain K Hydrophobic interactions: K:P.168, K:I.171 Hydrogen bonds: K:T.27, K:T.27, K:T.27, K:G.28, K:F.29, K:L.30, K:V.95, K:V.95, K:G.96, K:Y.145, K:K.149 Salt bridges: K:R.50, K:R.97, K:R.97, K:R.177, K:R.177 pi-Cation interactions: K:R.50

1 x ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate(Covalent)

ZMP.12: 16 residues within 4Å: Chain N: K.28, V.31, R.32, W.38, V.62, M.65, F.66, N.69, A.70, V.72, V.78, L.81, G.85, F.105 Chain Q: D.43, S.44 14 PLIP interactions: 12 interactions with chain N, 2 interactions with chain Q Hydrophobic interactions: N:W.38, N:W.38, N:M.65, N:F.66, N:V.78, N:F.105, N:F.105 Hydrogen bonds: N:K.28, N:N.69, N:N.69, Q:D.43, Q:S.44 Salt bridges: N:K.28, N:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Letts, J.A. et al., Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk. Mol.Cell (2019)

Release Date

2019-08-21

Peptides

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial: A
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial: B
NADH:ubiquinone oxidoreductase core subunit S1: C
NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2: D
NADH:ubiquinone oxidoreductase core subunit S3: E
NADH:ubiquinone oxidoreductase core subunit S7: F
NADH:ubiquinone oxidoreductase core subunit S8: G
NADH:ubiquinone oxidoreductase subunit V3: H
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial: I
NADH:ubiquinone oxidoreductase subunit S4: J
NADH:ubiquinone oxidoreductase subunit A9: K
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2: L
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5: M
NADH:ubiquinone oxidoreductase subunit A6: N
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7: O
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12: P
Acyl carrier protein: Q
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V1

B
V2

C
S1

D
S2

E
S3

F
S7

G
S8

H
V3

I
S6

J
S4

K
A9

L
A2

M
A5

N
A6

O
A7

P
AL

Q
AA

R
AM

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH:ubiquinone oxidoreductase core subunit S1

NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2

NADH:ubiquinone oxidoreductase core subunit S3

NADH:ubiquinone oxidoreductase core subunit S7

NADH:ubiquinone oxidoreductase core subunit S8

NADH:ubiquinone oxidoreductase subunit V3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

NADH:ubiquinone oxidoreductase subunit S4

NADH:ubiquinone oxidoreductase subunit A9

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

NADH:ubiquinone oxidoreductase subunit A6

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

Acyl carrier protein

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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