SMTL ID : 6qcf.1

Ovine respiratory complex I FRC open class 6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: S.359, C.360, G.361, Q.362, C.363, C.366, T.404, I.405, C.406 0 PLIP interactions: SF4.4: 8 residues within 4Å: Chain C: D.104, C.105, C.108, Q.110, C.114, L.116, V.205, G.206 0 PLIP interactions: SF4.5: 8 residues within 4Å: Chain C: C.153, I.154, Q.155, C.156, T.157, R.158, C.159, C.203 0 PLIP interactions: SF4.7: 9 residues within 4Å: Chain F: A.53, C.54, C.55, G.90, S.118, C.119, G.148, C.149, P.150 0 PLIP interactions: SF4.8: 7 residues within 4Å: Chain G: C.87, C.116, I.117, Y.118, C.119, G.120, C.122 0 PLIP interactions: SF4.9: 10 residues within 4Å: Chain G: C.77, I.78, A.79, C.80, K.81, L.82, C.83, C.126, A.130, I.131 0 PLIP interactions:

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 14 residues within 4Å: Chain A: G.68, R.69, G.70, A.72, F.74, N.97, D.99, E.100, G.101, G.188, E.189, V.223, N.225, A.407 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.407 Hydrogen bonds: A:R.69, A:R.69, A:G.70, A:D.99, A:D.99, A:G.101

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

FES.3: 10 residues within 4Å: Chain A: P.103, G.104 Chain B: C.103, T.105, C.108, C.144, L.145, G.146, A.147, C.148 0 PLIP interactions: FES.6: 7 residues within 4Å: Chain C: C.41, Y.42, G.50, C.52, R.53, C.55, C.69 0 PLIP interactions:

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 3 residues within 4Å: Chain I: C.59, C.84, C.87 No protein-ligand interaction detected (PLIP)

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

NDP.11: 9 residues within 4Å: Chain K: T.27, G.28, F.29, V.95, G.96, R.97, A.169, D.170, I.171 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:T.27, K:G.28, K:F.29, K:L.30, K:V.95, K:V.95, K:G.96, K:R.97, K:I.171, K:I.171

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

ZMP.12: 7 residues within 4Å: Chain N: M.65, F.66, N.69, A.70, H.71, V.72 Chain Q: S.44 4 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain N Hydrogen bonds: Q:S.44, N:F.66 Hydrophobic interactions: N:M.65, N:A.70 ZMP.13: 11 residues within 4Å: Chain 0: S.44, L.45 Chain c: R.46, F.47, H.50, K.51, A.59, L.62, A.66, E.69, F.70 5 PLIP interactions: 3 interactions with chain c, 2 interactions with chain 0 Hydrophobic interactions: c:A.59, c:A.66, c:F.70 Hydrogen bonds: 0:S.44, 0:L.45

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
NDUFS2: D
NADH:ubiquinone oxidoreductase core subunit S3: E
NDUFS7: F
NDUFS8: G
NDUFV3: H
NDUFS6: 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: Q0
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 1: S
NADH-ubiquinone oxidoreductase chain 6: T
NADH-ubiquinone oxidoreductase chain 4L: U
NADH-ubiquinone oxidoreductase chain 5: V
NADH-ubiquinone oxidoreductase chain 4: W
NADH-ubiquinone oxidoreductase chain 2: X
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: Y
NADH:ubiquinone oxidoreductase subunit B5: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 1
NDUFB10: 2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 3
NADH:ubiquinone oxidoreductase subunit S5: 4
NADH:ubiquinone oxidoreductase subunit A3: 5
NADH:ubiquinone oxidoreductase subunit B3: 6
NADH dehydrogenase [ubiquinone] 1 subunit C2: 7
NADH:ubiquinone oxidoreductase subunit B4: 8
NDUFA13: 9
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: a
NADH:ubiquinone oxidoreductase subunit B7: b
NADH:ubiquinone oxidoreductase subunit B9: c
NADH:ubiquinone oxidoreductase subunit B2: d
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: e
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: f
NDUFC1: g
NDUFB1: h
NDUFA1: i

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

0
AB

R
D3

S
D1

T
D6

U
4L

V
D5

W
D4

X
D2

Y
AK

Z
B5

1
A8

2
BJ

3
AJ

4
S5

5
A3

6
B3

7
C2

8
B4

9
AM

a
B6

b
B7

c
B9

d
B2

e
B8

f
BK

g
C1

h
B1

i
A1

Membrane

We predict this structure to be a membrane protein.
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NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

NADH:ubiquinone oxidoreductase core subunit S1

NDUFS2

NADH:ubiquinone oxidoreductase core subunit S3

NDUFS7

NDUFS8

NDUFV3

NDUFS6

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-ubiquinone oxidoreductase chain 3

NADH-ubiquinone oxidoreductase chain 1

NADH-ubiquinone oxidoreductase chain 6

NADH-ubiquinone oxidoreductase chain 4L

NADH-ubiquinone oxidoreductase chain 5

NADH-ubiquinone oxidoreductase chain 4

NADH-ubiquinone oxidoreductase chain 2

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

NADH:ubiquinone oxidoreductase subunit B5

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

NDUFB10

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial

NADH:ubiquinone oxidoreductase subunit S5

NADH:ubiquinone oxidoreductase subunit A3

NADH:ubiquinone oxidoreductase subunit B3

NADH dehydrogenase [ubiquinone] 1 subunit C2

NADH:ubiquinone oxidoreductase subunit B4

NDUFA13

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

NADH:ubiquinone oxidoreductase subunit B7

NADH:ubiquinone oxidoreductase subunit B9

NADH:ubiquinone oxidoreductase subunit B2

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial

NDUFC1

NDUFB1

NDUFA1

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