SMTL ID : 3m9s.2 (1 other biounit)

Crystal structure of respiratory complex I from Thermus thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.50 Å

Oligo State

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

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: P.199, S.352, C.353, G.354, K.355, C.356, C.359, S.398, F.399, C.400, L.402, A.403 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.353, A:C.356, A:C.359, A:C.400 SF4.4: 12 residues within 4Å: Chain C: H.115, D.118, C.119, C.122, K.124, G.125, C.128, L.130, Q.131, V.232, G.233 Chain D: I.325 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.118 Metal complexes: C:H.115, C:C.119, C:C.122, C:C.128 SF4.5: 11 residues within 4Å: Chain C: C.181, I.182, C.184, R.186, C.187, F.202, C.230, P.231, V.232, A.234, L.235 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.181, C:C.184, C:C.187, C:C.230 SF4.6: 11 residues within 4Å: Chain C: C.256, L.258, C.259, V.261, G.262, C.263, I.290, C.291, G.294, P.407, I.408 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.256, C:C.259, C:C.263, C:C.291 SF4.8: 13 residues within 4Å: Chain D: R.84, H.169 Chain F: C.45, C.46, G.82, R.83, G.109, A.110, C.111, F.118, G.139, C.140, P.141 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.45, F:C.46, F:C.111, F:C.140 SF4.9: 11 residues within 4Å: Chain G: H.41, C.63, P.64, I.68, C.98, I.99, F.100, C.101, G.102, L.103, C.104 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.63, G:C.98, G:C.101, G:C.104 SF4.10: 12 residues within 4Å: Chain G: C.53, I.54, G.55, C.56, S.57, L.58, C.59, C.108, P.109, T.110, A.112, I.113 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.53, G:C.56, G:C.59, G:C.108

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 19 residues within 4Å: Chain A: G.64, R.65, G.66, A.68, T.72, K.75, N.92, D.94, S.96, Y.180, G.183, E.184, E.185, I.218, N.219, N.220, T.223, P.401, L.402 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.180, A:E.184, A:E.184, A:P.401, A:L.402 Hydrogen bonds: A:R.65, A:G.66, A:K.75, A:N.92, A:D.94, A:D.94, A:S.96, A:E.185, A:N.219, A:N.220, A:N.220 Salt bridges: A:K.75

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

FES.3: 9 residues within 4Å: Chain B: C.83, T.85, S.87, C.88, C.124, L.125, G.126, S.127, C.128 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.83, B:C.88, B:C.124, B:C.128 FES.7: 11 residues within 4Å: Chain C: L.32, F.33, C.34, S.35, G.43, A.44, C.45, R.46, M.47, C.48, C.83 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.45, C:C.48, C:C.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Efremov, R.G. et al., The architecture of respiratory complex I. Nature (2010)

Release Date

2010-05-26

Peptides

NADH-quinone oxidoreductase subunit 1: A
NADH-quinone oxidoreductase subunit 2: B
NADH-quinone oxidoreductase subunit 3: C
NADH-quinone oxidoreductase subunit 4: D
NADH-quinone oxidoreductase subunit C: E
NADH-quinone oxidoreductase subunit B: F
NADH-quinone oxidoreductase subunit I: G
NADH-quinone oxidoreductase subunit 15: H
NADH-quinone oxidoreductase subunit 12: I
NADH-quinone oxidoreductase subunit 13: J
NADH-quinone oxidoreductase subunit 14: K
NADH-quinone oxidoreductase subunits 7, 10 and 11: L
NADH-quinone oxidoreductase subunit 8: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
J

I
O

J
P

K
Q

L
S

M
T

NADH-quinone oxidoreductase subunit 1

NADH-quinone oxidoreductase subunit 2

NADH-quinone oxidoreductase subunit 3

NADH-quinone oxidoreductase subunit 4

NADH-quinone oxidoreductase subunit C

NADH-quinone oxidoreductase subunit B

NADH-quinone oxidoreductase subunit I

NADH-quinone oxidoreductase subunit 15

NADH-quinone oxidoreductase subunit 12

NADH-quinone oxidoreductase subunit 13

NADH-quinone oxidoreductase subunit 14

NADH-quinone oxidoreductase subunits 7, 10 and 11

NADH-quinone oxidoreductase subunit 8

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