SMTL ID : 6uex.2 (1 other biounit)

Crystal structure of S. aureus LcpA in complex with octaprenyl-pyrophosphate-GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x Q5S: 2-(acetylamino)-2-deoxy-1-O-[(S)-hydroxy{[(S)-hydroxy{[(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]oxy}phosphoryl]oxy}phosphoryl]-alpha-D-glucopyranose(Non-covalent)

Q5S.1: 30 residues within 4Å: Chain A: I.31, V.33, G.35, D.37, R.45, D.47, S.48, M.50, V.52, M.61, R.68, V.112, D.113, F.114, F.117, M.120, N.140, I.141, L.158, A.161, R.162, R.164, R.173, Q.177, V.180, M.181, K.185, L.204, I.212 Ligands: GOL.9 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.31, A:V.33, A:D.47, A:V.112, A:F.114, A:F.117, A:F.117, A:I.141, A:L.158, A:A.161, A:V.180, A:K.185, A:I.212 Hydrogen bonds: A:R.45, A:D.47 Water bridges: A:R.164 Salt bridges: A:R.45, A:R.68, A:R.162, A:R.173 Q5S.11: 30 residues within 4Å: Chain B: I.31, V.33, G.35, D.37, R.45, D.47, S.48, M.50, V.52, M.61, R.68, V.112, D.113, F.114, F.117, M.120, N.140, I.141, L.158, A.161, R.162, R.164, R.173, Q.177, V.180, M.181, K.185, L.204, I.212 Ligands: GOL.19 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.31, B:V.33, B:D.47, B:V.112, B:F.114, B:F.117, B:F.117, B:I.141, B:L.158, B:A.161, B:V.180, B:K.185, B:I.212 Hydrogen bonds: B:R.45, B:D.47 Water bridges: B:R.164 Salt bridges: B:R.45, B:R.68, B:R.162, B:R.173

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

SO4.2: 5 residues within 4Å: Chain A: S.138, K.139, N.140, I.141, G.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.140, A:N.140, A:G.142 SO4.3: 3 residues within 4Å: Chain A: H.150, R.151 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.149, A:R.151 Salt bridges: A:H.150 SO4.4: 5 residues within 4Å: Chain A: S.144, K.146, H.150, E.156 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.146 Salt bridges: A:H.150 SO4.5: 1 residues within 4Å: Chain A: R.151 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.151 SO4.6: 7 residues within 4Å: Chain A: K.38, G.42 Chain B: A.36, S.44, Y.86, V.111, D.113 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.38 Hydrogen bonds: B:Y.86, B:D.113, B:D.113 Water bridges: B:D.113 SO4.7: 7 residues within 4Å: Chain A: S.30, Q.53, G.103, I.104, N.105, P.106, L.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.30, A:Q.53, A:G.103, A:N.105 SO4.8: 3 residues within 4Å: Chain A: A.39, Q.40, R.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.40 Water bridges: A:Q.43, A:Q.43 Salt bridges: A:R.45 SO4.12: 5 residues within 4Å: Chain B: S.138, K.139, N.140, I.141, G.142 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.140, B:N.140, B:G.142 SO4.13: 3 residues within 4Å: Chain B: H.150, R.151 Ligands: SO4.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.149, B:R.151 Salt bridges: B:H.150 SO4.14: 5 residues within 4Å: Chain B: S.144, K.146, H.150, E.156 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.146 Salt bridges: B:H.150 SO4.15: 1 residues within 4Å: Chain B: R.151 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.151 SO4.16: 7 residues within 4Å: Chain A: A.36, S.44, Y.86, V.111, D.113 Chain B: K.38, G.42 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.38 Hydrogen bonds: A:Y.86, A:Y.86, A:D.113 Water bridges: A:D.113 SO4.17: 7 residues within 4Å: Chain B: S.30, Q.53, G.103, I.104, N.105, P.106, L.270 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.30, B:Q.53, B:G.103, B:N.105 SO4.18: 3 residues within 4Å: Chain B: A.39, Q.40, R.45 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.40 Water bridges: B:Q.43, B:Q.43 Salt bridges: B:R.45

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: D.47, S.48, M.67, R.68, D.170, R.173, V.174, Q.177 Ligands: Q5S.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.68, A:D.170, A:D.170, A:R.173, A:Q.177 GOL.10: 3 residues within 4Å: Chain A: R.164, G.169, D.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.164, A:D.170, A:D.170 Water bridges: A:D.170 GOL.19: 9 residues within 4Å: Chain B: D.47, S.48, M.67, R.68, D.170, R.173, V.174, Q.177 Ligands: Q5S.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.68, B:D.170, B:R.173, B:Q.177 GOL.20: 3 residues within 4Å: Chain B: R.164, G.169, D.170 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.164, B:D.170, B:D.170 Water bridges: B:D.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, F.K.K. et al., Crystallographic analysis ofStaphylococcus aureusLcpA, the primary wall teichoic acid ligase. J.Biol.Chem. (2020)

Release Date

2020-01-29

Peptides

Regulatory protein MsrR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Regulatory protein MsrR

Related Entries With Identical Sequence