SMTL ID : 6i33.1

Crystal structure of human glycine decarboxylase (P-protein)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: Y.118, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.608, A:K.711 Hydrogen bonds: A:Y.118, A:T.340, A:T.340, A:S.514, A:G.575, A:A.576, A:E.579, A:N.708 Water bridges: A:C.339 Salt bridges: A:H.710, A:K.711 pi-Stacking: A:H.608 PLP.8: 16 residues within 4Å: Chain B: Y.118, C.339, T.340, S.514, S.574, G.575, A.576, E.579, H.608, T.610, D.684, A.686, H.706, N.708, H.710, K.711 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.608, B:K.711 Hydrogen bonds: B:Y.118, B:Y.118, B:C.339, B:T.340, B:T.340, B:S.574, B:G.575, B:A.576, B:T.610, B:N.708 Salt bridges: B:H.710 pi-Stacking: B:H.608

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

EDO.2: 3 residues within 4Å: Chain A: W.87, D.543, Q.544 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.544 EDO.3: 5 residues within 4Å: Chain A: H.17, R.23, E.70, N.71 Chain B: H.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.23, A:R.23, A:E.70 EDO.4: 7 residues within 4Å: Chain A: P.604, S.606, I.633, I.654, T.655, S.658, T.659 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.606, A:T.655, A:T.655, A:T.659, A:T.659 EDO.5: 5 residues within 4Å: Chain A: I.86, N.97, K.531, N.535 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97, A:N.535 EDO.6: 6 residues within 4Å: Chain A: N.97, C.98, S.99, V.100, N.535 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.97, A:N.97, A:V.100, A:V.100 EDO.9: 6 residues within 4Å: Chain A: H.507, N.937, K.938, F.939 Chain B: K.497, N.500 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.500 EDO.10: 5 residues within 4Å: Chain A: H.356 Chain B: H.17, D.18, R.23, E.70 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:S.99, A:E.431, B:D.19 Hydrogen bonds: B:R.23, B:R.23 EDO.11: 4 residues within 4Å: Chain A: A.526, W.530 Chain B: Q.102, L.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.102 EDO.12: 5 residues within 4Å: Chain B: N.97, C.98, S.99, V.100, N.535 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.97, B:C.98, B:V.100 Water bridges: B:N.535

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

BCT.7: 4 residues within 4Å: Chain A: F.417, R.418, L.419, F.539 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.419, A:F.539

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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