SMTL ID : 8bty.1

Structure of the active form of ScpB, the C5a-peptidase from Streptococcus agalactiae.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x MLA: MALONIC ACID(Covalent)

MLA.1: 5 residues within 4Å: Chain A: R.209, L.240, P.241, D.242, E.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.242 Salt bridges: A:R.209

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

SO4.2: 5 residues within 4Å: Chain A: G.263, N.264, G.479, T.480, S.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.264, A:T.480, A:S.481 Water bridges: A:S.481, A:S.481 SO4.5: 5 residues within 4Å: Chain A: V.831, T.832, E.833, Q.834, K.854 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.833, A:Q.834, A:Q.834 Salt bridges: A:K.854 SO4.6: 6 residues within 4Å: Chain A: Y.702, H.703, E.704, L.723, K.724, N.725 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.704, A:N.725, A:N.725 Water bridges: A:N.726, A:N.841 Salt bridges: A:H.703 SO4.7: 5 residues within 4Å: Chain A: R.660, K.662, K.667, E.668, E.669 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.669 Water bridges: A:R.660, A:K.662, A:K.662 Salt bridges: A:R.660, A:K.662 SO4.8: 4 residues within 4Å: Chain A: N.453, I.454, K.565, H.567 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.453, A:I.454 Water bridges: A:K.565, A:K.565 Salt bridges: A:K.565 SO4.9: 2 residues within 4Å: Chain A: L.646, R.679 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.679 SO4.10: 3 residues within 4Å: Chain A: M.505, P.507, R.510 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.510 SO4.11: 4 residues within 4Å: Chain A: G.746, V.747, E.748, N.749 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.746, A:E.748, A:N.749 SO4.12: 4 residues within 4Å: Chain A: R.915, N.951, E.952, D.953 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.952, A:D.953, A:D.953 Salt bridges: A:R.915 SO4.13: 2 residues within 4Å: Chain A: R.329 Ligands: EPE.14 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.329 SO4.15: 3 residues within 4Å: Chain A: H.279, E.689, K.690 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.690 Salt bridges: A:H.279

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: S.791, N.793, D.795, N.797, D.799 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.791, A:D.795, A:N.797, A:D.799, H2O.3

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

NA.4: 5 residues within 4Å: Chain A: M.519, S.520, A.522, A.541, S.672 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.522, A:S.672

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

EPE.14: 10 residues within 4Å: Chain A: K.179, E.180, E.308, S.326, R.329, L.466, Y.474, A.475, K.476 Ligands: SO4.13 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.179, A:K.476 Water bridges: A:S.326, A:R.329 Salt bridges: A:E.180, A:E.180, A:E.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cullen, R. et al., The 1.7 angstrom crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis. Proteins (2024)

Release Date

2023-11-15

Peptides

C5a peptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C5a peptidase