- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-mer
- Ligands
- 6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
FMN.2: 23 residues within 4Å:- Chain A: G.110, R.111, G.112, G.113, A.114, K.121, N.139, D.141, E.142, E.144, D.150, Y.227, G.230, E.231, E.232, V.265, T.266, N.267, T.270, T.374, A.449, L.450, A.453
17 PLIP interactions:17 interactions with chain A- Hydrophobic interactions: A:Y.227, A:E.231, A:E.231, A:A.449, A:A.453
- Hydrogen bonds: A:R.111, A:G.112, A:G.113, A:A.114, A:G.115, A:K.121, A:N.139, A:E.144, A:D.150, A:V.265, A:N.267
- Salt bridges: A:K.121
- 2 x T7X: Phosphatidylinositol(Non-covalent)
T7X.3: 14 residues within 4Å:- Chain B: W.56, D.462, R.463, N.464, L.467, M.471, F.475
- Chain L: L.12, T.16, Q.17, P.32, H.35, M.39
- Ligands: CDL.4
12 PLIP interactions:4 interactions with chain L, 8 interactions with chain B- Hydrophobic interactions: L:L.12, L:L.12, L:T.16, L:Q.17, B:L.467, B:M.471, B:F.475
- Hydrogen bonds: B:R.463, B:R.463, B:N.464, B:N.464
- Salt bridges: B:R.463
T7X.15: 11 residues within 4Å:- Chain 3: R.82, A.85, V.86, G.89
- Chain 6: L.25, L.29
- Chain Z: T.46, Y.49, L.50, I.53
- Ligands: CDL.4
3 PLIP interactions:1 interactions with chain 3, 1 interactions with chain Z, 1 interactions with chain 6- Salt bridges: 3:R.82
- Hydrogen bonds: Z:Y.49
- Hydrophobic interactions: 6:L.29
- 1 x CDL: CARDIOLIPIN(Non-covalent)
CDL.4: 18 residues within 4Å:- Chain 3: I.93
- Chain 5: F.13
- Chain 6: A.21, L.22, L.25, G.26
- Chain B: W.56, R.463
- Chain L: R.30, H.31, P.32, E.34, H.35
- Chain Z: T.46, V.47, L.50
- Ligands: T7X.3, T7X.15
8 PLIP interactions:3 interactions with chain Z, 1 interactions with chain 5, 1 interactions with chain 6, 1 interactions with chain L, 1 interactions with chain B, 1 interactions with chain 3- Hydrophobic interactions: Z:T.46, Z:V.47, Z:L.50, 5:F.13, 6:L.22, 3:I.93
- Salt bridges: L:R.30, B:R.463
- 1 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)
PEV.5: 17 residues within 4Å:- Chain E: F.191, I.192, F.203, V.283, F.287, Y.290, L.298, V.302, F.303, L.306
- Chain J: V.16
- Chain N: R.197, Q.201
- Chain X: T.70, L.71, L.73, M.76
14 PLIP interactions:9 interactions with chain E, 2 interactions with chain X, 3 interactions with chain N- Hydrophobic interactions: E:F.191, E:I.192, E:I.192, E:F.203, E:V.283, E:F.287, E:Y.290, E:L.298, E:F.303, X:L.73, X:L.73
- Salt bridges: N:R.197, N:R.197, N:R.197
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.8: 9 residues within 4Å:- Chain O: R.104, F.105, C.106, Y.107, C.117, R.118, C.120, A.132, C.134
4 PLIP interactions:4 interactions with chain O,- Metal complexes: O:C.106, O:C.117, O:C.117, O:C.134
FES.10: 9 residues within 4Å:- Chain R: C.130, P.134, C.135, C.171, M.172, G.173, C.174, C.175, M.180
5 PLIP interactions:5 interactions with chain R,- Metal complexes: R:C.130, R:C.135, R:C.171, R:C.174, R:C.175
- 1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NDP.9: 22 residues within 4Å:- Chain P: G.75, T.77, G.78, F.79, L.80, R.100, P.125, L.144, I.145, G.146, R.147, F.154, A.159, V.183, C.185, K.200, P.219, A.220, T.221, M.222, R.228, I.229
14 PLIP interactions:14 interactions with chain P- Hydrogen bonds: P:G.75, P:T.77, P:T.77, P:T.77, P:F.79, P:L.80, P:L.144, P:G.146, P:M.222
- Salt bridges: P:R.100, P:R.147, P:R.147, P:R.228
- pi-Cation interactions: P:R.100
- 2 x ZN: ZINC ION(Non-covalent)
ZN.11: 4 residues within 4Å:- Chain T: C.72, H.82, C.97, C.100
3 PLIP interactions:3 interactions with chain T- Metal complexes: T:C.72, T:H.82, T:C.97
ZN.16: 3 residues within 4Å:- Chain 5: H.107
- Chain 6: H.130
- Ligands: BCT.17
2 PLIP interactions:1 interactions with chain 5, 1 interactions with chain 6- Metal complexes: 5:H.107, 6:H.130
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Soufari, H. et al., Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Nat Commun (2020)
- Release Date
- 2020-10-28
- Peptides
- 51kDa: A
Nad2m: B
Nad3m: C
Nad6m: D
Nad1m: E
Nad4Lm: F
PGIV: G
B16.6: H
MWFE: I
B9: J
B14.5a: K
B14.5b: L
15kDa: M
Nad7m: N
75kDa: O
39kDa: P
Nad9m: Q
24kDa: R
18kDa: S
13kDa: T
B13: U
B17.2: V
PSST: W
TYKY: X
B14: Y
MNLL: Z
B8: 0
ACPM1: 1
Unk1: 2
P2: 3
CAL1: 4
CA1: 56
GLDH: 7 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
IC
JD
NE
HF
KG
YH
ZI
VJ
WK
SL
iM
jN
GO
CP
TQ
FR
BS
OT
PU
RV
UW
EX
DY
XZ
c0
Q1
k2
r3
n4
o5
q6
p7
z - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-mer
- Ligands
- 6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 2 x T7X: Phosphatidylinositol(Non-covalent)
- 1 x CDL: CARDIOLIPIN(Non-covalent)
- 1 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Soufari, H. et al., Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Nat Commun (2020)
- Release Date
- 2020-10-28
- Peptides
- 51kDa: A
Nad2m: B
Nad3m: C
Nad6m: D
Nad1m: E
Nad4Lm: F
PGIV: G
B16.6: H
MWFE: I
B9: J
B14.5a: K
B14.5b: L
15kDa: M
Nad7m: N
75kDa: O
39kDa: P
Nad9m: Q
24kDa: R
18kDa: S
13kDa: T
B13: U
B17.2: V
PSST: W
TYKY: X
B14: Y
MNLL: Z
B8: 0
ACPM1: 1
Unk1: 2
P2: 3
CAL1: 4
CA1: 56
GLDH: 7 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
IC
JD
NE
HF
KG
YH
ZI
VJ
WK
SL
iM
jN
GO
CP
TQ
FR
BS
OT
PU
RV
UW
EX
DY
XZ
c0
Q1
k2
r3
n4
o5
q6
p7
z - Membrane
-
We predict this structure to be a membrane protein.