- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.27 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x 1VU: propionyl Coenzyme A(Non-covalent)
- 28 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 8 residues within 4Å:- Chain A: G.189, A.190, T.191
- Chain B: A.239, A.240, K.267
- Ligands: EDO.22, EDO.26
Ligand excluded by PLIPEDO.3: 7 residues within 4Å:- Chain A: V.55, A.56, A.57, K.60
- Chain B: Q.282, G.287, M.298
Ligand excluded by PLIPEDO.4: 4 residues within 4Å:- Chain A: I.74, D.75, L.76, K.81
Ligand excluded by PLIPEDO.5: 3 residues within 4Å:- Chain A: K.302
- Chain C: D.183, S.187
Ligand excluded by PLIPEDO.6: 6 residues within 4Å:- Chain A: H.17, Y.19, F.173, D.175, G.214, Q.216
Ligand excluded by PLIPEDO.7: 4 residues within 4Å:- Chain A: D.53, K.114
- Chain B: M.298, K.302
Ligand excluded by PLIPEDO.8: 3 residues within 4Å:- Chain A: P.21, D.45, P.78
Ligand excluded by PLIPEDO.9: 3 residues within 4Å:- Chain A: K.205
- Chain B: K.157
- Ligands: EDO.36
Ligand excluded by PLIPEDO.10: 6 residues within 4Å:- Chain A: E.33, I.36, R.66, K.69, T.70, I.74
Ligand excluded by PLIPEDO.11: 4 residues within 4Å:- Chain A: E.98, Q.102, H.131, K.133
Ligand excluded by PLIPEDO.12: 3 residues within 4Å:- Chain A: N.58, K.59
- Chain B: Q.283
Ligand excluded by PLIPEDO.21: 3 residues within 4Å:- Chain B: E.116, T.149, S.187
Ligand excluded by PLIPEDO.22: 7 residues within 4Å:- Chain B: K.267, Q.303, N.306, T.307, L.310
- Ligands: EDO.2, EDO.26
Ligand excluded by PLIPEDO.23: 4 residues within 4Å:- Chain B: E.273, A.276, A.277
- Ligands: PGE.33
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain B: H.281, T.290
- Ligands: EDO.27, PGE.33
Ligand excluded by PLIPEDO.25: 3 residues within 4Å:- Chain B: Y.19, S.313
- Ligands: PEG.32
Ligand excluded by PLIPEDO.26: 7 residues within 4Å:- Chain B: Q.260, S.262, P.263, K.267, L.310
- Ligands: EDO.2, EDO.22
Ligand excluded by PLIPEDO.27: 5 residues within 4Å:- Chain B: T.290, F.291, Q.292
- Ligands: EDO.24, PGE.33
Ligand excluded by PLIPEDO.28: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPEDO.29: 3 residues within 4Å:- Chain B: P.265, E.266, K.269
Ligand excluded by PLIPEDO.30: 2 residues within 4Å:- Chain B: R.135, K.136
Ligand excluded by PLIPEDO.35: 3 residues within 4Å:- Chain C: V.88, E.119, W.123
Ligand excluded by PLIPEDO.36: 6 residues within 4Å:- Chain B: Y.201, K.205
- Chain C: L.154, K.205
- Ligands: EDO.9, PO4.19
Ligand excluded by PLIPEDO.37: 7 residues within 4Å:- Chain C: Y.19, D.175, G.214, Q.216
- Ligands: EDO.39, PGE.44, PG4.45
Ligand excluded by PLIPEDO.38: 4 residues within 4Å:- Chain C: H.281, F.289, T.290
- Ligands: 1VU.20
Ligand excluded by PLIPEDO.39: 5 residues within 4Å:- Chain C: H.17, Y.19
- Ligands: EDO.37, PEG.43, PGE.44
Ligand excluded by PLIPEDO.40: 3 residues within 4Å:- Chain C: W.270, F.291, L.300
Ligand excluded by PLIPEDO.41: 8 residues within 4Å:- Chain C: Y.19, P.21, R.22, R.23, Q.216, T.244, L.310
- Ligands: PG4.45
Ligand excluded by PLIP- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.13: 4 residues within 4Å:- Chain A: A.311, T.312, S.313, I.314
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:A.311
PEG.14: 3 residues within 4Å:- Chain A: V.88, S.89, W.123
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.89
PEG.15: 4 residues within 4Å:- Chain A: E.72, D.73, R.104, V.105
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.73
PEG.31: 5 residues within 4Å:- Chain A: T.191, S.192
- Chain B: W.270, I.296, L.300
No protein-ligand interaction detected (PLIP)PEG.32: 5 residues within 4Å:- Chain A: S.187
- Chain B: K.211, G.214, L.215
- Ligands: EDO.25
2 PLIP interactions:2 interactions with chain B- Water bridges: B:K.211, B:K.211
PEG.42: 4 residues within 4Å:- Chain C: A.311, T.312, S.313, I.314
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:A.311
PEG.43: 4 residues within 4Å:- Chain C: H.17, F.173
- Ligands: EDO.39, PGE.44
2 PLIP interactions:2 interactions with chain C- Water bridges: C:H.17, C:H.17
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.16: 4 residues within 4Å:- Chain A: E.94, W.123, K.127, F.130
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.94, A:W.123, A:K.127
PGE.33: 8 residues within 4Å:- Chain B: A.277, H.281, F.289, T.290, F.291
- Ligands: EDO.23, EDO.24, EDO.27
No protein-ligand interaction detected (PLIP)PGE.44: 10 residues within 4Å:- Chain C: L.164, P.168, F.173, L.174, F.213, G.214, L.215
- Ligands: EDO.37, EDO.39, PEG.43
1 PLIP interactions:1 interactions with chain C- Water bridges: C:L.174
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.17: 7 residues within 4Å:- Chain A: Y.19, K.211, G.214, L.215, T.309, S.313
- Chain C: S.187
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:S.313, C:S.187
- Water bridges: A:K.211, A:K.211
PG4.18: 9 residues within 4Å:- Chain A: E.266, K.267, W.270, F.291, S.294, I.296, L.300
- Chain C: T.191, S.192
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.266, A:F.291
PG4.45: 11 residues within 4Å:- Chain B: S.187
- Chain C: Y.19, K.211, G.214, L.215, Q.216, T.244, T.309, S.313
- Ligands: EDO.37, EDO.41
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:S.313
- Water bridges: C:K.211, C:K.211
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.19: 7 residues within 4Å:- Chain A: Y.201, K.205
- Chain B: Y.201, K.205
- Chain C: Y.201, K.205
- Ligands: EDO.36
13 PLIP interactions:6 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: A:Y.201, A:Y.201, C:Y.201
- Water bridges: A:K.205, A:K.205, A:K.205, B:K.205, C:Y.201, C:K.205
- Salt bridges: A:K.205, B:K.157, B:K.205, C:K.205
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shen, H. et al., The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell (2017)
- Release Date
- 2017-11-01
- Peptides
- Citrate lyase subunit beta-like protein, mitochondrial: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.27 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x 1VU: propionyl Coenzyme A(Non-covalent)
- 28 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shen, H. et al., The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12. Cell (2017)
- Release Date
- 2017-11-01
- Peptides
- Citrate lyase subunit beta-like protein, mitochondrial: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
C