SMTL ID : 3nyy.1

Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

6 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.1: 5 residues within 4Å: Chain A: F.5, Q.70, W.71, N.73, Q.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.70, A:Q.74 2PE.2: 9 residues within 4Å: Chain A: H.125, E.152, L.156, Y.172, Y.174, Y.222, T.227, E.228, E.229 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.228 Hydrogen bonds: A:E.229 2PE.3: 5 residues within 4Å: Chain A: K.134, N.135 Chain B: S.24, E.25, T.26 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.25, B:T.26 Water bridges: B:Y.44, B:E.51, B:E.51, B:E.51, B:E.51 2PE.8: 5 residues within 4Å: Chain B: F.5, Q.70, W.71, N.73, Q.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.70, B:Q.74 2PE.9: 9 residues within 4Å: Chain B: H.125, E.152, L.156, Y.172, Y.174, Y.222, T.227, E.228, E.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.228 Hydrogen bonds: B:E.229 Water bridges: B:Y.172 2PE.10: 5 residues within 4Å: Chain A: S.24, E.25, T.26 Chain B: K.134, N.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.25, A:T.26, A:T.26 Water bridges: A:E.51, A:E.51, A:E.51

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

SO4.4: 3 residues within 4Å: Chain A: R.19, R.117, R.123 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.19, A:R.19, A:G.124, A:E.228 Salt bridges: A:R.19, A:R.117 SO4.5: 4 residues within 4Å: Chain A: Y.68, W.77, V.81, R.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.68, A:W.77 Water bridges: A:D.78 Salt bridges: A:R.85 SO4.6: 3 residues within 4Å: Chain A: S.60, P.61, S.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.62, A:S.62 SO4.7: 2 residues within 4Å: Chain A: R.53, R.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.54 Water bridges: A:R.53 Salt bridges: A:R.53, A:R.54 SO4.11: 3 residues within 4Å: Chain B: R.19, R.117, R.123 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.19, B:R.19, B:G.124, B:E.228 Salt bridges: B:R.19, B:R.117 SO4.12: 4 residues within 4Å: Chain B: Y.68, W.77, V.81, R.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.77 Water bridges: B:Y.68 Salt bridges: B:R.85 SO4.13: 3 residues within 4Å: Chain B: S.60, P.61, S.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.62, B:S.62 SO4.14: 2 residues within 4Å: Chain B: R.53, R.54 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.54 Water bridges: B:R.53 Salt bridges: B:R.53, B:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution. To be published

Release Date

2010-09-15

Peptides

Putative glycyl-glycine endopeptidase lytM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative glycyl-glycine endopeptidase lytM