SMTL ID : 1knw.1

Crystal structure of diaminopimelate decarboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.271 Ligands: MES.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:S.344, A:R.271 Hydrogen bonds: A:R.271 SO4.6: 2 residues within 4Å: Chain B: R.271 Ligands: MES.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.271 Water bridges: B:R.271, A:S.344

4 x LI: LITHIUM ION(Non-covalent)

LI.2: 5 residues within 4Å: Chain A: H.151, S.152, K.154, N.156, N.161 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.151, A:S.152, A:K.154, H2O.91 LI.3: 6 residues within 4Å: Chain A: N.303, S.384, N.385, R.389, P.390, L.391 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.384, A:R.389, H2O.36 LI.7: 5 residues within 4Å: Chain B: H.151, S.152, K.154, N.156, N.161 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.151, B:S.152, B:K.154, H2O.484 LI.8: 6 residues within 4Å: Chain B: N.303, S.384, N.385, R.389, P.390, L.391 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.384, B:R.389, H2O.429

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

PLP.4: 14 residues within 4Å: Chain A: A.52, K.54, D.73, T.100, H.191, G.226, G.227, E.268, P.269, G.270, R.271, Y.378 Chain B: C.342 Ligands: MES.5 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.52, A:K.54, A:T.100 Hydrogen bonds: A:G.227, A:E.268, A:G.270, A:R.271, A:Y.378 Water bridges: A:D.73, A:L.228, A:R.271, A:R.271, A:R.271, A:F.272, B:C.342 Salt bridges: A:H.191 pi-Stacking: A:H.191 PLP.9: 14 residues within 4Å: Chain A: C.342 Chain B: A.52, K.54, D.73, T.100, H.191, G.226, G.227, E.268, P.269, G.270, R.271, Y.378 Ligands: MES.10 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.52, B:K.54, B:T.100 Hydrogen bonds: B:G.227, B:G.270, B:R.271 Water bridges: B:L.228, B:R.271, B:R.271, B:R.271, B:F.272, A:C.342 Salt bridges: B:H.191 pi-Stacking: B:H.191

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 11 residues within 4Å: Chain A: K.54, T.157, H.191, Y.311, Y.378, M.382 Chain B: E.343, S.344, Y.386 Ligands: SO4.1, PLP.4 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:H.191, A:R.271, A:R.271, B:S.344 Salt bridges: A:K.54, A:H.191, B:E.343 Hydrogen bonds: B:S.344, B:S.344 MES.10: 11 residues within 4Å: Chain A: E.343, S.344, Y.386 Chain B: K.54, T.157, H.191, Y.311, Y.378, M.382 Ligands: SO4.6, PLP.9 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Water bridges: B:H.191, B:R.271, B:R.271, A:S.344 Salt bridges: B:K.54, B:H.191, A:E.343 Hydrogen bonds: A:S.344, A:S.344

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

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