SMTL ID : 4lhc.1

Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

5 x GLY: GLYCINE(Non-covalent)

GLY.1: 6 residues within 4Å: Chain A: Y.134, C.353, C.530, H.623, K.726, W.870 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.134, A:Y.134, A:T.867 Salt bridges: A:H.623 GLY.2: 5 residues within 4Å: Chain A: I.352, C.353, H.623, G.624, T.625 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.624, A:T.625 Water bridges: A:S.350, A:I.352 Salt bridges: A:H.623 GLY.3: 6 residues within 4Å: Chain A: L.928, I.929, G.931, W.933, Q.939 Chain B: Q.939 9 PLIP interactions: 3 Ligand-Ligand interactions, 3 interactions with chain A, 3 interactions with chain B Water bridges: G.3, G.3, G.3, A:W.933, B:Q.939, B:Q.939 Hydrogen bonds: A:G.931, A:Q.939, B:Q.939 GLY.4: 6 residues within 4Å: Chain A: N.647, V.677, E.679, A.680, G.827, N.828 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.647, A:N.647, A:A.680, A:N.828 Water bridges: A:E.645, A:T.681, A:T.681, A:N.828 GLY.18: 6 residues within 4Å: Chain B: Y.134, C.353, C.530, H.623, K.726, W.870 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.134, B:Y.134, B:H.623

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

BCT.5: 7 residues within 4Å: Chain A: S.523, F.861, G.862, F.863, E.888, R.891, W.948 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.888, A:E.888 BCT.6: 7 residues within 4Å: Chain A: S.82, Y.84, G.85 Chain B: I.112, E.446, T.447, T.449 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.446, A:S.82, A:S.82 BCT.19: 7 residues within 4Å: Chain B: S.523, F.861, G.862, F.863, E.888, R.891, W.948 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.861, B:E.888

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 4 residues within 4Å: Chain A: D.581, K.745, S.746, H.747 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.746, A:H.747 Water bridges: A:D.718, A:H.747 Salt bridges: A:H.747 PO4.8: 4 residues within 4Å: Chain A: Q.76, L.77, P.78, W.573 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.76, A:W.573 PO4.9: 6 residues within 4Å: Chain A: T.151, D.155, D.494, S.973, C.974, E.975 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.494, A:S.973, A:E.975 Water bridges: A:Q.493, A:Q.493 PO4.20: 4 residues within 4Å: Chain B: D.581, K.745, S.746, H.747 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.746, B:H.747 Water bridges: B:D.718 Salt bridges: B:H.747 PO4.21: 4 residues within 4Å: Chain B: Q.76, L.77, P.78, W.573 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.76, B:Q.76 PO4.22: 6 residues within 4Å: Chain B: T.151, D.155, D.494, S.973, C.974, E.975 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.494, B:S.973, B:E.975 Water bridges: B:D.155, B:D.155, B:D.155, B:Q.493

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

EDO.10: 5 residues within 4Å: Chain A: D.894, A.898, P.945, A.946, P.947 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.294, T.544, W.545, P.546, G.549, K.550 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: F.71, P.72, R.73, S.74 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: F.71, P.72, R.73, R.711, D.714 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: D.252, H.255, G.280 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: Q.797, T.800, K.801 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: L.52, N.811, A.814, E.818, R.826, E.830, L.831 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: P.294, T.544, W.545, P.546, G.549, K.550 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: E.42, Q.45, L.49, T.56, L.57, K.801 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: L.52, K.815, E.830, L.831 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: D.894, A.898, P.945, A.946, P.947 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: S.229, H.257, Q.258 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: P.753, R.754, T.755 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: I.69, R.70, F.71, P.72, C.710, R.711, D.714, F.715 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: E.571, T.755, Y.778 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: D.912, D.915, P.936 Ligand excluded by PLIP

1 x BCN: BICINE(Non-covalent)

BCN.16: 7 residues within 4Å: Chain A: Q.98, F.100, E.426, P.556, A.557, G.558, Q.559 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.558, A:Q.559 Salt bridges: A:E.426

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasse, D. et al., Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation. J.Biol.Chem. (2013)

Release Date

2013-10-16

Peptides

Glycine dehydrogenase [decarboxylating]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycine dehydrogenase [decarboxylating]

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