SMTL ID : 6i35.2 (1 other biounit)

Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 19 residues within 4Å: Chain A: Y.118, Y.121, C.339, T.340, S.514, C.515, S.574, G.575, A.576, E.579, H.608, T.610, D.684, A.686, N.687, N.708, H.710, K.711 Ligands: GOL.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.608, A:A.686 Hydrogen bonds: A:Y.118, A:Y.121, A:T.340, A:S.514, A:S.514, A:G.575, A:A.576, A:T.610, A:N.708 Water bridges: A:C.339 Salt bridges: A:H.608, A:H.710 pi-Stacking: A:H.608 PLG.7: 16 residues within 4Å: Chain B: Y.118, Y.121, C.339, T.340, S.514, S.574, G.575, A.576, E.579, H.608, T.610, D.684, A.686, N.708, H.710, K.711 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:H.608, B:A.686 Hydrogen bonds: B:Y.118, B:Y.118, B:T.340, B:T.340, B:S.514, B:S.514, B:S.574, B:G.575, B:A.576, B:E.579, B:N.708 Water bridges: B:C.339 Salt bridges: B:H.608, B:H.710 pi-Stacking: B:H.608

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: R.23 Chain B: H.356, H.359, H.486 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.359 EDO.8: 5 residues within 4Å: Chain A: H.356 Chain B: H.17, D.18, R.23, E.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.17, B:R.23, B:R.23, B:E.70

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.121, Q.327, H.328, C.339, H.608, W.854 Ligands: PLG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.121, A:Y.121, A:Q.327, A:Q.327 GOL.5: 7 residues within 4Å: Chain A: H.17, D.18, R.23, E.70, N.71 Chain B: S.99, H.356 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.23, A:R.23 Water bridges: A:R.23, B:V.100, B:H.356

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: M.93, F.417, R.418, L.419, F.539, V.742 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.417, A:R.418, A:R.418, A:L.419 PEG.6: 7 residues within 4Å: Chain A: H.507, N.937, K.938, F.939 Chain B: K.497, N.500 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.500 Water bridges: B:K.497 PEG.9: 7 residues within 4Å: Chain B: N.500, K.501, K.938, F.939, W.940, T.942 Ligands: PEG.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.937, B:W.940, A:N.500

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Laer, B. et al., Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant. To Be Published

Release Date

2019-11-20

Peptides

Glycine dehydrogenase (decarboxylating), mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Glycine dehydrogenase (decarboxylating), mitochondrial

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