SMTL ID : 2z2p.1

Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x MHW- THR- DBB- PRO- MHU- MHV- 004- MHT: Quinupristin(Non-covalent)

MHW-THR-DBB-PRO-MHU-MHV-004-MHT.1: 22 residues within 4Å: Chain A: Y.18, H.33, K.58, M.60, Y.102, M.117, Y.142, S.144, N.159, Q.160, A.182, G.184, V.186, I.201, I.202, R.226, H.228, W.243, E.268, E.284 Ligands: MG.3, DOL.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.18, A:Y.102, A:Y.102, A:A.182, A:V.186, A:I.202, A:W.243, A:W.243 Hydrogen bonds: A:K.58, A:R.226, A:R.226, A:E.268, A:E.284 Salt bridges: A:H.228 MHW-THR-DBB-PRO-MHU-MHV-004-MHT.2: 27 residues within 4Å: Chain A: D.24, S.66, E.106, P.108, L.148, N.152 Chain B: Y.18, H.33, M.60, Y.102, M.117, Y.142, S.144, N.159, Q.160, A.182, G.184, V.186, I.201, I.202, R.226, H.228, W.243, E.268, E.284 Ligands: MG.6, DOL.8 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.18, B:Y.102, B:Y.102, B:A.182, B:V.186, B:W.243, B:W.243, A:P.108 Hydrogen bonds: B:Y.18, B:K.58, B:R.226, B:E.284, A:S.66 Salt bridges: B:H.228, A:D.24

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.268, E.284 Ligands: MHW-THR-DBB-PRO-MHU-MHV-004-MHT.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.268, A:E.284 MG.4: 5 residues within 4Å: Chain A: S.65, D.67, E.69, W.71, D.127 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.67, A:E.69, A:D.127, A:D.127 MG.6: 3 residues within 4Å: Chain B: E.268, E.284 Ligands: MHW-THR-DBB-PRO-MHU-MHV-004-MHT.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.268, B:E.284 MG.7: 4 residues within 4Å: Chain B: D.67, E.69, W.71, D.127 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.67, B:E.69, B:D.127, B:D.127

2 x DOL: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE(Non-covalent)

DOL.5: 6 residues within 4Å: Chain A: K.34, W.243, S.266, E.268, C.285 Ligands: MHW-THR-DBB-PRO-MHU-MHV-004-MHT.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.243 Hydrogen bonds: A:K.34 Salt bridges: A:E.268 DOL.8: 12 residues within 4Å: Chain A: P.108, N.109, D.151, N.152, T.168, E.169 Chain B: K.34, W.243, G.244, S.266, E.268 Ligands: MHW-THR-DBB-PRO-MHU-MHV-004-MHT.2 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.243, A:N.152, A:E.169 Hydrogen bonds: B:K.34 Salt bridges: B:E.268, A:E.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korczynska, M. et al., Structural Basis for Streptogramin B Resistance in Staphylococcus Aureus by Virginiamycin B Lyase. Proc.Natl.Acad.Sci.USA (2007)

Release Date

2007-06-19

Peptides

Virginiamycin B lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Virginiamycin B lyase