SMTL ID : 1ko0.1

Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 16 residues within 4Å: Chain A: A.52, K.54, D.73, T.100, H.189, H.191, G.226, G.227, E.268, P.269, G.270, R.271, Y.378 Chain B: C.342 Ligands: LYS.2, DLY.3 22 PLIP interactions: 19 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:A.52, A:K.54, A:T.100, K.2 Hydrogen bonds: A:K.54, A:G.227, A:E.268, A:G.270, A:R.271, A:Y.378, K.2 Water bridges: A:D.73, A:D.73, A:R.142, A:L.228, A:L.228, A:R.271, A:R.271, A:R.271 Salt bridges: A:H.191, K.2 pi-Stacking: A:H.191 PLP.4: 16 residues within 4Å: Chain A: C.342 Chain B: A.52, K.54, D.73, T.100, H.189, H.191, G.226, G.227, E.268, P.269, G.270, R.271, Y.378 Ligands: LYS.5, DLY.6 20 PLIP interactions: 17 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:A.52, B:K.54, B:T.100, K.5 Hydrogen bonds: B:G.227, B:G.270, B:R.271, K.5 Water bridges: B:K.54, B:K.54, B:R.142, B:L.228, B:L.228, B:R.271, B:R.271, B:R.271, B:R.271 Salt bridges: B:H.191, K.5 pi-Stacking: B:H.191

2 x LYS: LYSINE(Non-covalent)

LYS.2: 12 residues within 4Å: Chain A: K.54, H.191, R.271, R.307, Y.311, Y.378, M.382 Chain B: C.342, E.343, Y.386 Ligands: PLP.1, DLY.3 9 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.378, A:Y.378 Hydrogen bonds: A:H.191, A:Y.311, B:E.343, K.2, K.2 Salt bridges: A:R.271, A:R.307 LYS.5: 12 residues within 4Å: Chain A: C.342, E.343, Y.386 Chain B: K.54, H.191, R.271, R.307, Y.311, Y.378, M.382 Ligands: PLP.4, DLY.6 8 PLIP interactions: 5 interactions with chain B, 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: B:Y.378, B:Y.378 Hydrogen bonds: B:H.191, K.5, K.5, A:E.343 Salt bridges: B:R.271, B:R.307

2 x DLY: D-LYSINE(Non-covalent)

DLY.3: 12 residues within 4Å: Chain A: K.54, T.157, H.191, Y.311, Y.378, M.382 Chain B: C.342, E.343, S.344, Y.386 Ligands: PLP.1, LYS.2 9 PLIP interactions: 5 interactions with chain A, 3 Ligand-Ligand interactions, 1 interactions with chain B Hydrophobic interactions: A:Y.378, K.2, K.2 Hydrogen bonds: A:H.191, A:Y.311, A:Y.311, B:S.344 Salt bridges: A:H.191, K.2 DLY.6: 12 residues within 4Å: Chain A: C.342, E.343, S.344, Y.386 Chain B: K.54, T.157, H.191, Y.311, Y.378, M.382 Ligands: PLP.4, LYS.5 8 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.344, B:H.191, B:Y.311 Hydrophobic interactions: B:Y.378, K.5, K.5 Salt bridges: B:H.191, K.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Levdikov, V. et al., Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation. To be Published

Release Date

2003-11-11

Peptides

Diaminopimelate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diaminopimelate decarboxylase

Related Entries With Identical Sequence