SMTL ID : 1wyv.1 (1 other biounit)

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 16 residues within 4Å: Chain A: T.320, T.321 Chain B: S.73, A.131, G.132, A.133, E.136, H.166, S.168, T.210, D.239, A.241, N.263, H.265, K.266 Ligands: AOA.2 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.166, B:T.210, B:A.241 Hydrogen bonds: B:S.73, B:G.132, B:A.133, B:S.168, B:N.263, A:T.321, A:T.321 Salt bridges: B:H.265, B:K.266 pi-Stacking: B:H.166 Water bridges: A:T.320 PLP.3: 16 residues within 4Å: Chain C: T.320, T.321 Chain D: S.73, A.131, G.132, A.133, E.136, H.166, S.168, T.210, D.239, A.241, N.263, H.265, K.266 Ligands: AOA.4 13 PLIP interactions: 3 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:T.321, C:T.321, D:S.73, D:G.132, D:A.133, D:N.263 Water bridges: C:T.320 Hydrophobic interactions: D:H.166, D:T.210, D:A.241 Salt bridges: D:H.265, D:K.266 pi-Stacking: D:H.166

2 x AOA: (AMINOOXY)ACETIC ACID(Non-covalent)

AOA.2: 6 residues within 4Å: Chain A: Y.95, Y.98, Q.308, T.320 Chain B: H.166 Ligands: PLP.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.95, A:Y.98, A:Q.308 Water bridges: A:Y.95, B:K.266 AOA.4: 6 residues within 4Å: Chain C: Y.95, Y.98, Q.308, T.320 Chain D: H.166 Ligands: PLP.3 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.95, C:Y.98, C:Q.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakai, T. et al., Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. Embo J. (2005)

Release Date

2005-04-05

Peptides

glycine dehydrogenase (decarboxylating) subunit 1: AC
glycine dehydrogenase subunit 2 (P-protein): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

glycine dehydrogenase (decarboxylating) subunit 1

glycine dehydrogenase subunit 2 (P-protein)

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