SMTL ID : 3iam.1 (1 other biounit)

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-oligomer

Ligands

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

SF4.1: 10 residues within 4Å: Chain D: R.84, H.169 Chain F: C.45, C.46, G.82, R.83, A.110, C.111, 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 SF4.2: 12 residues within 4Å: Chain G: H.41, C.63, P.64, A.65, 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 SF4.3: 10 residues within 4Å: Chain G: C.53, I.54, G.55, C.56, S.57, C.59, C.108, 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 SF4.4: 10 residues within 4Å: Chain C: H.115, D.118, C.119, C.122, K.124, C.128, L.130, Q.131, V.232, G.233 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: 12 residues within 4Å: Chain C: C.181, I.182, H.183, C.184, R.186, C.187, F.202, C.230, P.231, V.232, A.234, L.235 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.181, C:C.184, C:C.184, C:C.187, C:C.230 SF4.6: 10 residues within 4Å: Chain C: C.256, L.258, C.259, V.261, G.262, C.263, I.290, C.291, 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: 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

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

FES.7: 9 residues within 4Å: Chain C: C.34, S.35, I.42, G.43, A.44, C.45, R.46, 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 FES.9: 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

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.10: 19 residues within 4Å: Chain A: G.64, R.65, G.66, A.68, T.72, K.75, N.92, D.94, E.95, S.96, G.183, E.184, E.185, I.218, N.219, N.220, T.223, P.401 Ligands: NAI.11 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.184, A:E.184, A:P.401 Hydrogen bonds: A:G.66, A:G.66, A:N.92, A:D.94, A:D.94, A:S.96, A:G.183, A:E.185, A:E.185, A:I.218, A:N.219, A:N.220, A:N.220 Salt bridges: A:K.75

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.11: 17 residues within 4Å: Chain A: G.66, G.67, A.68, F.70, K.75, F.78, E.95, S.96, E.97, Y.180, E.185, K.202, F.205, G.324, T.325, P.401 Ligands: FMN.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.97, A:Y.180, A:T.325 Hydrogen bonds: A:G.66, A:K.75, A:S.96, A:E.97, A:E.185 Salt bridges: A:K.202 pi-Stacking: A:F.70, A:F.205

6 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 2 residues within 4Å: Chain C: L.274, D.302 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:L.274, C:D.302, C:D.302 MG.13: 2 residues within 4Å: Chain C: H.167 Chain H: E.32 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.167, C:H.167 MG.14: 1 residues within 4Å: Chain E: H.144 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.144 MG.15: 1 residues within 4Å: Chain A: H.35 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.35 MG.17: 4 residues within 4Å: Chain D: V.223, A.384, K.386, E.388 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.388 MG.18: 4 residues within 4Å: Chain A: H.350 Chain B: S.68, V.122, E.123 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 6 residues within 4Å: Chain C: D.165, H.168 Chain H: E.32, E.34, S.60, G.64 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:G.64

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Berrisford, J.M. et al., Structural basis for the mechanism of respiratory complex I. J.Biol.Chem. (2009)

Release Date

2009-09-15

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 5: E
NADH-quinone oxidoreductase subunit 6: F
NADH-quinone oxidoreductase subunit 9: G
NADH-quinone oxidoreductase subunit 15: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
9

H
7

NADH-quinone oxidoreductase subunit 1

NADH-quinone oxidoreductase subunit 2

NADH-quinone oxidoreductase subunit 3

NADH-quinone oxidoreductase subunit 4

NADH-quinone oxidoreductase subunit 5

NADH-quinone oxidoreductase subunit 6

NADH-quinone oxidoreductase subunit 9

NADH-quinone oxidoreductase subunit 15

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