SMTL ID : 6i34.1 (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.6 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, A:K.711 Salt bridges: A:H.710, A:K.711 pi-Stacking: A:H.608 PLP.8: 15 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 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:H.608, B:A.686, B:K.711 Hydrogen bonds: B:Y.118, B:Y.118, B:T.340, B:T.340, B:S.514, B:S.574, B:G.575, B:A.576, B:T.610, B:N.708 Water bridges: B:C.339 Salt bridges: B:H.710, B:K.711 pi-Stacking: B:H.608

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

EDO.2: 4 residues within 4Å: Chain A: H.17, R.23, E.70 Ligands: EDO.10 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.23, A:R.23, A:E.70 Water bridges: A:H.17, B: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: 5 residues within 4Å: Chain A: R.60, P.61, K.63, E.561, R.696 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:R.696, A:R.696 Water bridges: A:K.59, A:K.63, A:K.63 EDO.9: 4 residues within 4Å: Chain A: H.356 Chain B: H.17, R.23, E.70 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:S.99, A:H.356, A:E.431 Hydrogen bonds: B:R.23, B:R.23 EDO.10: 8 residues within 4Å: Chain A: H.17, D.18, R.23 Chain B: H.356, G.360, H.363, I.364 Ligands: EDO.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.23, A:R.23, B:G.360 EDO.11: 5 residues within 4Å: Chain A: R.23 Chain B: Y.355, H.356, H.359, H.486 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.355, B:H.359

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

PEG.5: 7 residues within 4Å: Chain A: N.500, H.507, N.937, K.938, F.939 Chain B: K.497, N.500 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.500, B:N.500 Water bridges: A:E.936, A:W.940, B:K.497, B:K.497 PEG.12: 5 residues within 4Å: Chain A: N.500 Chain B: N.937, K.938, F.939, W.940 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.500, B:W.940 Water bridges: A:K.497, A:K.497, B:E.936

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: Y.121, G.513, S.514, C.515, H.608, K.711, T.851, W.854 Ligands: PLP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.711, A:T.851 GOL.7: 7 residues within 4Å: Chain A: R.8, L.10, E.11, L.14, P.15, R.16 Chain B: E.435 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.8, A:P.15, B:E.435

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
A

B
B

Neanderthal Glycine decarboxylase

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