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

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

Coordinates

PDB Format

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, T.655, D.684, A.686, N.708, H.710, K.711 Ligands: GOL.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.608, A:T.655, A:A.686 Hydrogen bonds: A:Y.118, A:Y.118, A:T.340, A:T.340, A:S.514, A:S.514, A:G.575, A:A.576, A:E.579, A:N.708 Salt bridges: A:H.608, A:H.710 pi-Stacking: A:H.608 PLG.8: 20 residues within 4Å: Chain B: Y.118, Y.121, C.339, T.340, S.514, C.515, S.574, G.575, A.576, E.579, H.608, T.610, T.655, D.684, A.686, N.687, H.706, N.708, H.710, K.711 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:H.608, B:T.655, B:A.686 Hydrogen bonds: B:Y.118, B:Y.121, B:C.339, B:T.340, B:T.340, B:S.514, B:S.514, B:S.514, B:S.514, B:G.575, B:A.576, B:N.708 Water bridges: B:S.574 Salt bridges: B:H.608, B:H.710 pi-Stacking: B:H.608

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

EDO.2: 5 residues within 4Å: Chain A: N.500, K.938, F.939 Chain B: N.500 Ligands: PEG.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:N.500, B:N.500 Hydrogen bonds: A:N.500, A:K.938 EDO.6: 5 residues within 4Å: Chain A: R.23 Chain B: H.356, H.359, G.360, H.486 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Y.121, Q.327, H.328, H.608 Ligands: PLG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.327, A:Q.327 Water bridges: A:T.851 GOL.4: 7 residues within 4Å: Chain A: H.17, D.18, R.23, E.70, N.71 Chain B: S.99, H.356 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.23, A:R.23, A:E.70, B:H.356 Water bridges: B:S.99, B:V.100 GOL.9: 7 residues within 4Å: Chain A: S.99, H.356 Chain B: H.17, D.18, R.23, E.70, N.71 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.23, B:R.23 Water bridges: B:D.18, A:V.100, A:H.356, A:H.356, A:H.356, A:E.431

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.5: 4 residues within 4Å: Chain A: F.417, R.418, L.419, F.539 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.419

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

PEG.7: 6 residues within 4Å: Chain A: N.500 Chain B: N.500, N.937, K.938, F.939 Ligands: EDO.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.500, A:N.500 Water bridges: B:W.940, A:K.497

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
A

B
B

Glycine dehydrogenase (decarboxylating), mitochondrial

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