SMTL ID : 3h41.1

CRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BACILLUS CEREUS ATCC 10987 AT 1.79 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ALA: ALANINE(Non-covalent)

ALA.1: 8 residues within 4Å: Chain A: L.60, E.61, Y.96, W.206, A.207, D.215, D.234 Ligands: DGL.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.206, A:A.207 Hydrogen bonds: A:E.61 Water bridges: A:E.61, A:Y.96

1 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.2: 8 residues within 4Å: Chain A: W.206, D.215, C.216, S.217, D.234, S.235, H.268 Ligands: ALA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.206 Hydrogen bonds: A:D.215, A:S.217, A:S.217, A:S.235 Water bridges: A:G.236, A:G.236

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: S.134, E.135, K.136, K.138, Q.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134, A:E.135, A:K.136, A:Q.166 Salt bridges: A:K.138

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 4 residues within 4Å: Chain A: I.193, N.194, K.197, I.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.194, A:N.194, A:K.197 PG4.5: 6 residues within 4Å: Chain A: L.25, A.33, T.34, D.78, P.101, K.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.103 Water bridges: A:D.78 PG4.6: 7 residues within 4Å: Chain A: D.12, L.66, I.131, L.140, L.162, P.163, N.164 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.164 Water bridges: A:S.139 PG4.7: 6 residues within 4Å: Chain A: G.236, P.237, S.239, R.240, G.265, S.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.239, A:R.240 Water bridges: A:V.267, A:V.267 PG4.8: 7 residues within 4Å: Chain A: N.132, S.152, D.154, I.156, S.157, R.159, W.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.152, A:S.152, A:S.157 Water bridges: A:R.159 PG4.9: 9 residues within 4Å: Chain A: M.46, T.47, L.48, K.51, P.203, A.285, E.286, R.287, S.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.288 Water bridges: A:K.51, A:K.51, A:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-[gamma]-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr.,Sect.F (2010)

Release Date

2009-05-05

Peptides

NLP/P60 family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NLP/P60 family protein