SMTL ID : 6i34.2 (1 other biounit)

Crystal structure of Neanderthal glycine decarboxylase (P-protein)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 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 Ligands: GOL.8 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:T.610, A:N.708 Water bridges: A:C.339 Salt bridges: A:H.710, A:K.711 pi-Stacking: A:H.608 PLP.10: 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, N.708, H.710, K.711 Ligands: GOL.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.608, B:A.686, B:K.711 Hydrogen bonds: B:Y.118, B:T.340, B:T.340, B:S.514, B:G.575, B:A.576, B:E.579, B:N.708, B:K.711 Water bridges: B:C.339 Salt bridges: B:H.710, B:K.711 pi-Stacking: B:H.608

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

EDO.2: 6 residues within 4Å: Chain A: N.97, C.98, L.254, R.276, D.430, E.431 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.97, A:R.276, A:E.431, A:E.431 EDO.3: 5 residues within 4Å: Chain A: M.93, F.417, R.418, L.419, V.742 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.417, A:L.419 EDO.4: 8 residues within 4Å: Chain A: Q.165, D.332, A.334, S.336, N.337, A.613, H.616, M.617 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.165, A:A.334, A:A.334 EDO.11: 8 residues within 4Å: Chain A: H.17, D.18, R.23 Chain B: H.356, G.360, H.363, I.364 Ligands: PEG.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.356, B:G.360, A:R.23 Water bridges: A:D.19 EDO.12: 5 residues within 4Å: Chain A: H.356 Chain B: H.17, D.18, R.23, E.70 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:S.99, A:S.99, A:V.100 Hydrogen bonds: B:R.23, B:R.23, B:E.70

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

PEG.5: 6 residues within 4Å: Chain A: N.500, H.507, N.937, K.938, F.939 Chain B: N.500 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.500, B:N.500 Water bridges: A:W.940, B:K.497, B:N.500 PEG.6: 9 residues within 4Å: Chain A: H.17, D.18, R.23, E.70, N.71 Chain B: S.99, V.100, H.356 Ligands: EDO.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.23, A:E.70, B:V.100 PEG.9: 5 residues within 4Å: Chain A: N.500 Chain B: N.500, N.937, K.938, F.939 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Water bridges: B:N.500, B:E.936, B:W.940, B:W.940, A:K.497, A:K.497 Hydrogen bonds: A:N.500

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: R.8, E.11, L.14, P.15, R.16 Chain B: E.435 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.8, A:E.11, A:P.15 Water bridges: B:E.435, B:E.435, B:E.435 GOL.8: 9 residues within 4Å: Chain A: Y.121, C.339, G.513, S.514, C.515, H.608, K.711, T.851 Ligands: PLP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.608, A:K.711, A:K.711, A:T.851 Water bridges: A:Q.327 GOL.13: 9 residues within 4Å: Chain B: Y.121, Q.327, H.328, C.339, S.514, H.608, K.711, W.854 Ligands: PLP.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.327, B:Q.327 Water bridges: B:Y.121, B:T.851

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

Neanderthal Glycine decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Neanderthal Glycine decarboxylase

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