SMTL ID : 4b52.1 (1 other biounit)

Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.135, H.139, E.159, H.219 Ligands: RDF.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.135, A:H.139, A:E.159, RDF.5, RDF.5

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.129, D.131, Q.170, D.178, D.179 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.129, A:D.131, A:D.178, H2O.7, H2O.8 CA.3: 3 residues within 4Å: Chain A: D.53, D.55, V.57 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.53, A:D.55, A:V.57, H2O.4, H2O.4 CA.4: 4 residues within 4Å: Chain A: Y.181, T.182, I.185, D.188 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.181, A:I.185, A:D.188, H2O.8, H2O.8

1 x RDF: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN(Non-covalent)

RDF.5: 15 residues within 4Å: Chain A: N.104, N.105, A.106, F.107, F.123, F.126, V.132, H.135, E.136, H.139, E.159, L.190, R.191, H.219 Ligands: ZN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.123, A:F.126, A:L.190 Hydrogen bonds: A:N.104, A:N.105, A:N.105, A:N.105, A:N.105, A:R.191, A:R.191 Water bridges: A:W.108, A:E.136 Salt bridges: A:H.219, A:H.219

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

NA.6: 2 residues within 4Å: Chain A: N.109, G.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruf, A. et al., Structure of Gentlyase, the Neutral Metalloprotease of Paenibacillus Polymyxa. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-01-09

Peptides

BACILLOLYSIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BACILLOLYSIN

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