SMTL ID : 3fdb.1

Crystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from corynebacterium diphtheriae at 1.99 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: D.89, V.90, I.191, A.220, S.222, K.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.90, A:S.222, A:S.222 NA.16: 6 residues within 4Å: Chain B: D.89, V.90, I.191, A.220, S.222, K.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.90, B:S.222 Water bridges: B:A.228, B:C.232

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: P.88, G.256 Chain B: P.88, G.256 Ligands: CL.17 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: V.30, A.31, R.352 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: C.38, P.39, A.40 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: D.89, R.92 Chain B: D.255, G.256 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: N.161, P.162, L.311, F.343, R.352 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: P.88, G.256 Chain B: P.88, G.256 Ligands: CL.2 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: V.30, A.31, R.352 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: C.38, P.39, A.40 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: D.255, G.256 Chain B: D.89, R.92 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: N.161, P.162, L.311, F.343, R.352 Ligand excluded by PLIP

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: P.5, S.6, I.7, S.358, E.360, V.361 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: F.197, V.280, A.281, K.284 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: A.341, W.342, G.344, E.345 Ligands: EDO.15 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.174, R.181 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Y.95, I.96, D.99, H.100 Chain B: Y.95 Ligands: EDO.26 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: F.316, R.317, T.319, I.321, G.323, P.325 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: M.16, Y.115, P.117 Chain B: Y.56 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: A.341, W.342 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: F.119, F.131, G.344, E.345 Ligands: EDO.9 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: P.5, S.6, I.7, S.358, E.360, V.361 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: F.197, V.280, A.281, K.284 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: A.341, W.342, G.344, E.345 Ligands: EDO.30 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: E.174, R.181 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: Y.95 Chain B: Y.95, I.96, D.99, H.100 Ligands: EDO.11 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: F.316, R.317, T.319, I.321, G.323, P.325 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: Y.56 Chain B: M.16, Y.115, P.117 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: A.341, W.342 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: F.119, F.131, G.344, E.345 Ligands: EDO.24 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative PLP-dependent beta-cystathionase (NP_940074.1) from CORYNEBACTERIUM DIPHTHERIAE at 1.99 A resolution. To be published

Release Date

2008-12-09

Peptides

putative PLP-dependent beta-cystathionase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

putative PLP-dependent beta-cystathionase