SMTL ID : 1m0o.1

Structure of Dialkylglycine Decarboxylase Complexed with 1-Amino-1-methylpropanephosphonate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.80, A:T.303, A:V.305, A:D.307, H2O.1 K.4: 5 residues within 4Å: Chain B: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.80, B:T.303, B:V.305, B:D.307, H2O.8 K.7: 5 residues within 4Å: Chain C: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.80, C:T.303, C:V.305, C:D.307, H2O.14 K.10: 5 residues within 4Å: Chain D: L.78, S.80, T.303, V.305, D.307 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.80, D:T.303, D:V.305, D:D.307, H2O.21

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: A.95, T.98, P.99, P.100, L.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.98, A:T.98, A:L.102, A:L.102 NA.5: 5 residues within 4Å: Chain B: A.95, T.98, P.99, P.100, L.102 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.98, B:T.98, B:T.98, B:L.102 NA.8: 5 residues within 4Å: Chain C: A.95, T.98, P.99, P.100, L.102 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.98, C:T.98, C:L.102 NA.11: 5 residues within 4Å: Chain D: A.95, T.98, P.99, P.100, L.102 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.98, D:T.98, D:L.102

4 x MPM: (1R)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]-1-METHYLPROPYLPHOSPHONIC ACID(Non-covalent)

MPM.3: 18 residues within 4Å: Chain A: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain C: Y.301, T.302, T.303 22 PLIP interactions: 6 interactions with chain C, 16 interactions with chain A Hydrophobic interactions: C:Y.301, A:W.138, A:W.138, A:E.210 Hydrogen bonds: C:T.303, C:T.303, A:Q.52, A:T.110, A:T.110, A:G.111, A:A.112, A:N.115, A:Q.246, A:K.272, A:K.272, A:R.406, A:R.406 Water bridges: C:Y.301, C:T.303, C:H.304, A:M.141, A:M.141 MPM.6: 18 residues within 4Å: Chain B: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain D: Y.301, T.302, T.303 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:W.138, B:W.138, B:E.210, D:Y.301 Hydrogen bonds: B:Q.52, B:T.110, B:T.110, B:G.111, B:A.112, B:N.115, B:Q.246, B:K.272, B:K.272, B:R.406, B:R.406, D:T.303, D:T.303 Water bridges: B:M.141, B:M.141, D:Y.301, D:T.303, D:H.304 MPM.9: 18 residues within 4Å: Chain A: Y.301, T.302, T.303 Chain C: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:W.138, C:W.138, C:E.210, A:Y.301 Hydrogen bonds: C:Q.52, C:T.110, C:G.111, C:A.112, C:N.115, C:Q.246, C:K.272, C:K.272, C:R.406, C:R.406, A:T.303, A:T.303, A:T.303 Water bridges: C:T.110, C:T.110, C:M.141, C:M.141, A:T.302, A:H.304 MPM.12: 18 residues within 4Å: Chain B: Y.301, T.302, T.303 Chain D: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 23 PLIP interactions: 17 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:W.138, D:W.138, D:E.210, B:Y.301 Hydrogen bonds: D:Q.52, D:T.110, D:G.111, D:A.112, D:N.115, D:Q.246, D:K.272, D:K.272, D:R.406, D:R.406, B:T.303, B:T.303, B:T.303 Water bridges: D:T.110, D:T.110, D:M.141, D:M.141, B:T.302, B:H.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, W. et al., Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition. Biochemistry (2002)

Release Date

2002-10-23

Peptides

2,2-Dialkylglycine decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

2,2-Dialkylglycine decarboxylase

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