SMTL ID : 5vxo.1

Crystal Structure Analysis of human CLYBL in complex with propionyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-trimer

Ligands

3 x 1VU: propionyl Coenzyme A(Non-covalent)

1VU.1: 22 residues within 4Å: Chain A: L.26, Y.27, V.28, P.29, K.34, K.35, K.38, D.50, D.53, G.54, R.84, V.221, F.225, R.226, I.249, H.250, P.251 Chain B: A.288, F.289, T.290, M.295, D.297 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:D.53, A:F.225, B:A.288, B:M.295 Hydrogen bonds: A:Y.27, A:K.34, A:R.226, A:I.249, B:D.297, B:D.297 Water bridges: A:K.35, B:T.290 Salt bridges: A:K.34, A:K.35, A:K.38, A:H.250 pi-Stacking: A:H.250 1VU.20: 22 residues within 4Å: Chain B: L.26, Y.27, V.28, P.29, K.34, K.35, K.38, D.50, D.53, G.54, R.84, V.221, I.249, H.250, P.251 Chain C: A.288, F.289, T.290, M.295, D.297, P.299 Ligands: EDO.38 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:D.53, C:A.288, C:M.295 Hydrogen bonds: B:Y.27, B:I.249, C:D.297 Water bridges: B:K.35, B:K.35, B:E.148 Salt bridges: B:K.34, B:K.35, B:K.38, B:H.250 pi-Stacking: B:H.250 1VU.34: 15 residues within 4Å: Chain A: A.288, M.295, D.297 Chain C: L.26, Y.27, V.28, K.34, K.35, K.38, G.54, R.84, V.221, I.249, H.250, P.251 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.249, A:A.288 Hydrogen bonds: C:Y.27, C:I.249, A:D.297 Water bridges: C:D.50, C:E.148, C:E.148 Salt bridges: C:K.34, C:K.35, C:K.38, C:H.250 pi-Cation interactions: C:K.35

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 PLIP EDO.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 PLIP EDO.4: 4 residues within 4Å: Chain A: I.74, D.75, L.76, K.81 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: K.302 Chain C: D.183, S.187 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: H.17, Y.19, F.173, D.175, G.214, Q.216 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: D.53, K.114 Chain B: M.298, K.302 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: P.21, D.45, P.78 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.205 Chain B: K.157 Ligands: EDO.36 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: E.33, I.36, R.66, K.69, T.70, I.74 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: E.98, Q.102, H.131, K.133 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: N.58, K.59 Chain B: Q.283 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: E.116, T.149, S.187 Ligand excluded by PLIP EDO.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 PLIP EDO.23: 4 residues within 4Å: Chain B: E.273, A.276, A.277 Ligands: PGE.33 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: H.281, T.290 Ligands: EDO.27, PGE.33 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: Y.19, S.313 Ligands: PEG.32 Ligand excluded by PLIP EDO.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 PLIP EDO.27: 5 residues within 4Å: Chain B: T.290, F.291, Q.292 Ligands: EDO.24, PGE.33 Ligand excluded by PLIP EDO.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: P.265, E.266, K.269 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain B: R.135, K.136 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: V.88, E.119, W.123 Ligand excluded by PLIP EDO.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 PLIP EDO.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 PLIP EDO.38: 4 residues within 4Å: Chain C: H.281, F.289, T.290 Ligands: 1VU.20 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain C: H.17, Y.19 Ligands: EDO.37, PEG.43, PGE.44 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain C: W.270, F.291, L.300 Ligand excluded by PLIP EDO.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
A

B
B

C
C

Citrate lyase subunit beta-like protein, mitochondrial

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