- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 2 residues within 4Å:- Chain A: K.25, R.27
4 PLIP interactions:4 interactions with chain A- Water bridges: A:K.25, A:R.27
- Salt bridges: A:K.25, A:R.27
SO4.3: 5 residues within 4Å:- Chain A: V.67, F.73, D.74, R.75, E.76
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.75, A:E.76
- Water bridges: A:A.68, A:A.68, A:F.73
- Salt bridges: A:R.75
SO4.17: 2 residues within 4Å:- Chain C: K.25, R.27
2 PLIP interactions:2 interactions with chain C- Salt bridges: C:K.25, C:R.27
SO4.18: 5 residues within 4Å:- Chain C: V.67, F.73, D.74, R.75, E.76
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:F.73, C:R.75, C:E.76
- Salt bridges: C:R.75
SO4.25: 3 residues within 4Å:- Chain D: G.159, K.160, E.170
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:K.160
- Salt bridges: D:K.153
- 9 x NA: SODIUM ION(Non-functional Binders)
NA.4: 5 residues within 4Å:- Chain A: L.128, E.143
- Chain B: R.104, E.137, Y.138
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:E.143, B:R.104
- Water bridges: B:R.104
NA.11: 5 residues within 4Å:- Chain B: I.7, R.104, I.105, E.108, R.109
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.104, B:E.108, B:R.109
NA.12: 5 residues within 4Å:- Chain B: K.153, L.158, G.159, L.169, E.170
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:G.159, B:L.169
NA.13: 3 residues within 4Å:- Chain A: P.24
- Chain B: Y.88, E.129
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.129
NA.14: 5 residues within 4Å:- Chain A: D.71, Q.126
- Chain B: G.178, H.344, E.345
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:H.344, A:D.71
- Water bridges: A:Q.126
NA.19: 2 residues within 4Å:- Chain C: V.87, P.124
No protein-ligand interaction detected (PLIP)NA.26: 1 residues within 4Å:- Chain D: K.154
No protein-ligand interaction detected (PLIP)NA.27: 2 residues within 4Å:- Chain D: Y.88, E.129
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Y.88, D:E.129
NA.28: 2 residues within 4Å:- Chain D: K.21, D.37
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:K.21, D:K.21
- 2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
SF4.5: 13 residues within 4Å:- Chain B: I.181, P.199, T.346, C.347, G.348, Q.349, C.350, C.353, S.391, I.392, C.393, L.395, G.396
4 PLIP interactions:4 interactions with chain B,- Metal complexes: B:C.347, B:C.350, B:C.353, B:C.393
SF4.20: 13 residues within 4Å:- Chain D: I.181, P.199, T.346, C.347, G.348, Q.349, C.350, C.353, S.391, I.392, C.393, L.395, G.396
4 PLIP interactions:4 interactions with chain D,- Metal complexes: D:C.347, D:C.350, D:C.353, D:C.393
- 2 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)
FNR.6: 20 residues within 4Å:- Chain B: G.65, R.66, G.67, K.76, N.92, D.94, E.95, S.96, Y.180, I.181, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395
- Ligands: AP0.7
20 PLIP interactions:20 interactions with chain B- Hydrophobic interactions: B:Y.180, B:I.181, B:E.184, B:E.184
- Hydrogen bonds: B:R.66, B:G.67, B:N.92, B:S.96, B:G.183, B:E.185, B:N.219, B:N.220, B:N.220, B:T.223
- Water bridges: B:G.70, B:N.92, B:E.95, B:Y.180, B:G.183
- Salt bridges: B:K.76
FNR.21: 20 residues within 4Å:- Chain D: G.65, R.66, G.67, K.76, N.92, D.94, E.95, S.96, Y.180, I.181, G.183, E.184, E.185, V.218, N.219, N.220, T.223, G.394, L.395
- Ligands: AP0.22
20 PLIP interactions:20 interactions with chain D- Hydrophobic interactions: D:Y.180, D:I.181, D:E.184, D:E.184, D:L.395
- Hydrogen bonds: D:R.66, D:G.67, D:N.92, D:D.94, D:S.96, D:G.183, D:E.185, D:N.219, D:N.220, D:N.220
- Water bridges: D:N.92, D:D.94, D:E.95, D:G.183
- Salt bridges: D:K.76
- 2 x AP0: ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED(Non-covalent)
AP0.7: 15 residues within 4Å:- Chain B: G.67, G.68, A.69, F.71, K.76, E.95, S.96, E.97, Y.180, E.185, Y.205, P.206, V.207, T.319
- Ligands: FNR.6
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:E.97, B:Y.180, B:T.319
- Hydrogen bonds: B:K.76, B:S.96, B:E.97
- Water bridges: B:Y.205, B:Y.205, B:G.394
- pi-Stacking: B:F.71, B:Y.205, B:Y.205
AP0.22: 16 residues within 4Å:- Chain D: G.67, G.68, A.69, F.71, K.76, F.79, E.95, S.96, E.97, Y.180, E.185, Y.205, P.206, V.207, T.319
- Ligands: FNR.21
12 PLIP interactions:12 interactions with chain D- Hydrophobic interactions: D:E.97, D:Y.180, D:T.319
- Hydrogen bonds: D:K.76, D:S.96, D:E.97
- Water bridges: D:E.184, D:E.184, D:G.394
- pi-Stacking: D:F.71, D:Y.205, D:Y.205
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 7 residues within 4Å:- Chain B: Y.34, D.37, G.38, G.39, E.116, P.228, F.229
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:E.116
- Water bridges: B:R.22, B:D.37, B:Y.40, B:A.42, B:S.232, B:S.232
GOL.9: 5 residues within 4Å:- Chain B: G.159, K.160, E.170
- Chain D: K.25, R.27
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain B- Hydrogen bonds: D:R.27, B:K.160, B:K.160, B:E.170
- Water bridges: D:E.33
GOL.10: 3 residues within 4Å:- Chain B: P.84, G.85, R.87
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.85, B:R.87, B:R.87
- Water bridges: B:V.81, B:G.126
GOL.23: 8 residues within 4Å:- Chain D: Y.34, D.37, G.38, G.39, E.116, P.228, F.229, S.232
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:E.116, D:S.232, D:S.232
- Water bridges: D:R.22, D:D.37, D:Y.40, D:Y.40
GOL.24: 1 residues within 4Å:- Chain D: R.87
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:R.87, D:R.87
- Water bridges: D:E.52, D:E.52, D:G.85
- 1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wohlwend, D. et al., Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I. Structure (2024)
- Release Date
- 2024-04-03
- Peptides
- NADH-quinone oxidoreductase subunit E: AC
NADH-quinone oxidoreductase subunit F: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CB
BD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 5 x SO4: SULFATE ION(Non-functional Binders)
- 9 x NA: SODIUM ION(Non-functional Binders)
- 2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)
- 2 x AP0: ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wohlwend, D. et al., Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I. Structure (2024)
- Release Date
- 2024-04-03
- Peptides
- NADH-quinone oxidoreductase subunit E: AC
NADH-quinone oxidoreductase subunit F: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CB
BD
D