SMTL ID : 3eif.1

1.9 angstrom crystal structure of the active form of the C5a peptidase from Streptococcus pyogenes (ScpA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.726, N.728, D.730, N.732, D.734 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.726, A:D.730, A:N.732, A:D.734, H2O.1

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

NA.2: 5 residues within 4Å: Chain A: M.454, S.455, A.457, A.476, S.607 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.476, A:S.607

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

SO4.3: 5 residues within 4Å: Chain A: R.595, K.597, K.602, E.603, E.604 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.604 Water bridges: A:Y.468, A:Y.468, A:R.595 Salt bridges: A:R.595, A:K.597 SO4.4: 4 residues within 4Å: Chain A: N.388, I.389, K.500, H.502 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.227, A:D.227, A:I.389 Water bridges: A:K.500, A:H.502, A:H.502 Salt bridges: A:K.500, A:H.502 SO4.5: 6 residues within 4Å: Chain A: Y.637, H.638, E.639, L.658, K.659, N.660 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.639, A:N.660 Water bridges: A:N.660, A:N.661, A:N.776 Salt bridges: A:H.638 SO4.6: 5 residues within 4Å: Chain A: V.766, T.767, E.768, Q.769, K.789 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.766, A:E.768, A:Q.769 Salt bridges: A:K.789 SO4.7: 4 residues within 4Å: Chain A: R.850, N.886, E.887, D.888 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.887, A:D.888 Water bridges: A:N.886, A:N.886 Salt bridges: A:R.850 SO4.8: 2 residues within 4Å: Chain A: L.581, R.614 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.614 Salt bridges: A:R.614 SO4.9: 5 residues within 4Å: Chain A: G.198, N.199, G.414, T.415, S.416 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.198, A:T.415, A:S.416, A:S.416 Water bridges: A:S.196, A:T.415, A:S.416, A:S.416

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 10 residues within 4Å: Chain A: K.114, E.115, P.116, E.243, S.261, R.264, L.401, Y.409, A.410, K.411 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.261, A:K.411 Water bridges: A:K.114, A:S.261, A:R.264 Salt bridges: A:E.115, A:E.115, A:E.243

1 x MLA: MALONIC ACID(Non-covalent)

MLA.11: 3 residues within 4Å: Chain A: R.297, D.301, F.302 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.302 Hydrogen bonds: A:D.301, A:F.302 Salt bridges: A:R.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kagawa, T.F. et al., Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 A Crystal Structure of the Active Form of ScpA. J.Mol.Biol. (2009)

Release Date

2009-02-24

Peptides

C5a peptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C5a peptidase