SMTL ID : 3g23.1

Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: E.196 Chain B: H.197, Y.199, A.200, R.203 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: H.197, Y.199, A.200, R.203 Chain B: M.170, E.196 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.76, V.129 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: S.45 Chain B: R.233 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: Y.199, D.232, R.233 Chain B: H.48 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: R.244, F.254 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.121 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: R.4, E.70, Q.100, R.121 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: A.150, R.151, E.152 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: G.93, R.94 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: G.1, M.2 Ligands: GOL.13 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: P.156, R.267 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: H.48 Chain B: Y.199, D.232, R.233 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: R.76, G.78, V.129 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: A.150, R.151, E.152 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: P.156, R.267 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain B: R.91 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain A: M.2, T.3, R.4, D.33, L.147, A.148, G.149 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.33 GOL.14: 5 residues within 4Å: Chain A: Y.115, R.118, P.182, D.183, H.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.116, A:D.183 GOL.15: 2 residues within 4Å: Chain A: R.17, F.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 GOL.16: 8 residues within 4Å: Chain A: H.198, V.228, P.229, E.230, N.231, D.232, R.233, F.235 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.198, A:E.230, A:D.232, A:R.233, A:F.235 Water bridges: A:H.198 GOL.17: 3 residues within 4Å: Chain A: S.226, D.227, V.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.227, A:D.227, A:V.228 Water bridges: A:S.226, A:S.226 GOL.24: 8 residues within 4Å: Chain B: H.198, V.228, P.229, E.230, N.231, D.232, R.233, F.235 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.198, B:E.230, B:D.232, B:D.232, B:R.233, B:F.235 Water bridges: B:H.198 GOL.25: 5 residues within 4Å: Chain B: S.210, A.213, W.246, R.249, A.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.210 Water bridges: B:S.210, B:R.249 GOL.26: 3 residues within 4Å: Chain B: S.226, D.227, V.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.227, B:D.227, B:V.228 Water bridges: B:V.228

1 x UNL: UNKNOWN LIGAND

UNL.18: 11 residues within 4Å: Chain A: M.170, A.173, M.174, L.204, H.207 Chain B: M.170, A.173, M.174, R.203, L.204, H.207 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.173 Water bridges: B:R.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, D. et al., Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling. J.Bacteriol. (2013)

Release Date

2009-02-10

Peptides

LD-carboxypeptidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

LD-carboxypeptidase A