SMTL ID : 1m0n.1

Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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.2 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.10 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.18 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.26

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:L.102, A:L.102 Water bridges: A:G.101 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:L.102 Water bridges: B:G.101 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:P.99, C:L.102 Water bridges: C:G.101 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:A.95, D:L.102 Water bridges: D:G.101

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

HCP.3: 19 residues within 4Å: Chain A: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain C: Y.301, T.302, T.303 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:W.138, A:E.210, A:K.272, C:Y.301 Hydrogen bonds: A:Q.52, A:Q.52, A:G.111, A:A.112, A:N.115, A:Q.246, A:K.272, A:R.406, A:R.406, C:T.303, C:T.303 Water bridges: A:W.138, A:M.141, A:E.210, C:T.303, C:T.303, C:H.304 HCP.6: 19 residues within 4Å: Chain B: Q.52, M.53, T.110, G.111, A.112, N.115, W.138, H.139, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 Chain D: Y.301, T.302, T.303 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: B:W.138, B:E.210, B:K.272, D:Y.301 Hydrogen bonds: B:Q.52, B:Q.52, B:G.111, B:A.112, B:N.115, B:Q.246, B:K.272, B:R.406, B:R.406, D:T.303, D:T.303 Water bridges: B:W.138, B:M.141, B:E.210, D:T.303, D:T.303, D:H.304 HCP.9: 19 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, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain C Hydrophobic interactions: A:Y.301, C:W.138, C:E.210, C:K.272 Hydrogen bonds: A:T.303, A:T.303, A:T.303, C:Q.52, C:Q.52, C:G.111, C:A.112, C:N.115, C:Q.246, C:K.272, C:R.406, C:R.406 Water bridges: A:H.304, C:T.110, C:W.138, C:M.141, C:E.210 HCP.12: 19 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, G.140, E.210, S.215, D.243, A.245, Q.246, K.272, R.406 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:W.138, D:E.210, D:K.272, B:Y.301 Hydrogen bonds: D:Q.52, D:Q.52, D:G.111, D:A.112, D:N.115, D:Q.246, D:K.272, D:R.406, D:R.406, B:T.303, B:T.303, B:T.303 Water bridges: D:T.110, D:W.138, D:M.141, D:E.210, 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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