SMTL ID : 3iib.1

Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.269, E.304, H.401, H.402 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.269, A:E.304, A:H.402, H2O.6, H2O.8 ZN.2: 6 residues within 4Å: Chain A: H.257, D.269, E.303, D.331, Y.397 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.257, A:D.269, A:D.331, H2O.6, H2O.6 ZN.6: 5 residues within 4Å: Chain B: D.269, E.304, H.401, H.402 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.269, B:E.304, B:H.402, H2O.30, H2O.32 ZN.7: 6 residues within 4Å: Chain B: H.257, D.269, E.303, D.331, Y.397 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.257, B:D.269, B:D.331, H2O.30, H2O.30

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: L.22, S.57, L.58, K.282, D.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.282, A:H.283 Water bridges: A:D.286 PGE.8: 5 residues within 4Å: Chain B: L.22, S.57, L.58, K.282, D.286 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.282, B:H.283 Water bridges: B:D.286

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: R.112, N.210, L.213, K.214 No protein-ligand interaction detected (PLIP) PEG.5: 2 residues within 4Å: Chain A: Y.24, P.413 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain B: R.112, N.210, L.213, K.214 No protein-ligand interaction detected (PLIP) PEG.10: 2 residues within 4Å: Chain B: Y.24, P.413 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution. To be published

Release Date

2009-08-25

Peptides

Peptidase M28: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptidase M28