SMTL ID : 4n31.1

Structure and activity of Streptococcus pyogenes SipA: a signal peptidase homologue essential for pilus polymerisation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.161, G.162 Chain B: K.153 Chain C: R.161 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Salt bridges: C:R.161, B:K.153 Hydrogen bonds: A:G.162 PO4.3: 4 residues within 4Å: Chain B: L.50, T.156 Chain C: V.160 Ligands: PTY.2 No protein-ligand interaction detected (PLIP) PO4.4: 4 residues within 4Å: Chain A: R.161 Chain C: R.161, G.162 Chain D: K.153 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:G.162 Salt bridges: A:R.161, D:K.153 PO4.6: 4 residues within 4Å: Chain A: V.160 Chain D: L.50, T.156 Ligands: PTY.5 No protein-ligand interaction detected (PLIP) PO4.7: 4 residues within 4Å: Chain E: R.161, G.162 Chain F: K.153 Chain G: R.161 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 1 interactions with chain E Salt bridges: F:K.153, G:R.161 Hydrogen bonds: E:G.162 PO4.9: 4 residues within 4Å: Chain F: L.50, T.156 Chain G: V.160 Ligands: PTY.8 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.156 PO4.10: 4 residues within 4Å: Chain E: R.161 Chain G: R.161, G.162 Chain H: K.153 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E, 1 interactions with chain H Hydrogen bonds: G:G.162 Salt bridges: E:R.161, H:K.153 PO4.12: 4 residues within 4Å: Chain E: V.160 Chain H: L.50, T.156 Ligands: PTY.11 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.156

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 18 residues within 4Å: Chain B: V.31, I.33, G.46, L.158, V.160, R.161 Chain C: V.31, G.48, V.49, L.50, L.158 Chain E: F.29, Y.52, K.153, S.155 Ligands: PO4.3, PTY.5, PTY.8 10 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C, 4 interactions with chain B, 3 interactions with chain E Water bridges: F:G.162, E:Y.52 Hydrophobic interactions: C:V.31, C:L.158, B:V.31, B:V.160, E:F.29 Hydrogen bonds: B:R.161, B:R.161 Salt bridges: E:K.153 PTY.5: 18 residues within 4Å: Chain A: V.31, G.48, V.49, L.50, L.158 Chain D: V.31, I.33, G.46, L.158, V.160, R.161 Chain G: F.29, Y.52, K.153, S.155 Ligands: PTY.2, PO4.6, PTY.11 10 PLIP interactions: 3 interactions with chain G, 4 interactions with chain D, 2 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: G:F.29, D:V.31, D:V.160, A:V.31, A:L.158 Water bridges: G:Y.52, H:G.162 Salt bridges: G:K.153 Hydrogen bonds: D:R.161, D:R.161 PTY.8: 18 residues within 4Å: Chain A: F.29, Y.52, K.153, S.155 Chain F: V.31, I.33, G.46, L.158, V.160, R.161 Chain G: V.31, G.48, V.49, L.50, L.158 Ligands: PTY.2, PO4.9, PTY.11 10 PLIP interactions: 4 interactions with chain F, 3 interactions with chain A, 2 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: F:V.31, F:V.160, A:F.29, G:V.31, G:L.158 Hydrogen bonds: F:R.161, F:R.161, A:Y.52 Salt bridges: A:K.153 Water bridges: B:G.162 PTY.11: 18 residues within 4Å: Chain C: F.29, Y.52, K.153, S.155 Chain E: V.31, G.48, V.49, L.50, L.158 Chain H: V.31, I.33, G.46, L.158, V.160, R.161 Ligands: PTY.5, PTY.8, PO4.12 10 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 3 interactions with chain C, 4 interactions with chain H Water bridges: D:G.162 Hydrophobic interactions: E:V.31, E:L.158, C:F.29, H:V.31, H:V.160 Hydrogen bonds: C:Y.52, H:R.161, H:R.161 Salt bridges: C:K.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Young, P.G. et al., Structure and activity of Streptococcus pyogenes SipA: a signal peptidase-like protein essential for pilus polymerisation. Plos One (2014)

Release Date

2014-08-20

Peptides

SipA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

SipA