SMTL ID : 5vxc.1

Crystal Structure Analysis of human CLYBL in complex with free CoASH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 17 residues within 4Å: Chain A: L.26, Y.27, V.28, K.34, K.35, K.38, G.54, R.84, F.225, I.249, H.250, P.251 Chain B: A.288, F.289, T.290, M.295, D.297 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.288, B:M.295, A:F.225, A:I.249 Hydrogen bonds: B:D.297, A:Y.27, A:I.249 Salt bridges: A:K.34, A:K.35, A:K.38, A:H.250 pi-Stacking: A:H.250 COA.3: 17 residues within 4Å: Chain B: L.26, Y.27, V.28, K.34, K.35, K.38, G.54, R.84, F.225, I.249, H.250, P.251 Chain C: A.288, F.289, T.290, M.295, D.297 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.225, B:I.249, C:A.288, C:M.295 Hydrogen bonds: B:Y.27, B:I.249, C:D.297 Salt bridges: B:K.34, B:K.35, B:K.38, B:H.250 pi-Stacking: B:H.250 COA.5: 17 residues within 4Å: Chain A: A.288, F.289, T.290, M.295, D.297 Chain C: L.26, Y.27, V.28, K.34, K.35, K.38, G.54, R.84, F.225, I.249, H.250, P.251 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.225, C:I.249, A:A.288, A:M.295 Hydrogen bonds: C:Y.27, C:I.249, A:D.297 Salt bridges: C:K.34, C:K.35, C:K.38, C:H.250 pi-Stacking: C:H.250

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.148, D.183 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.148, A:D.183, H2O.1, H2O.2, H2O.6 MG.4: 2 residues within 4Å: Chain B: E.148, D.183 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.148, B:D.183, H2O.9, H2O.10, H2O.14 MG.6: 2 residues within 4Å: Chain C: E.148, D.183 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.148, C:D.183, H2O.17, H2O.18, H2O.21

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
A

C
A

Citrate lyase subunit beta-like protein, mitochondrial

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