SMTL ID : 4dz3.1

Crystal structure of a Peptidyl-prolyl cis-trans isomerase with surface mutation M61H from Burkholderia pseudomallei complexed with FK506

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x FK5: 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN(Non-covalent)

FK5.1: 13 residues within 4Å: Chain A: Y.33, F.43, D.44, R.49, F.53, H.61, V.62, I.63, W.66, G.88, Y.89, I.98, F.106 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.33, A:F.53, A:F.53, A:F.53, A:F.53, A:V.62, A:W.66, A:W.66, A:Y.89, A:I.98 Hydrogen bonds: A:I.63, A:Y.89 FK5.7: 14 residues within 4Å: Chain B: Y.33, F.43, D.44, R.49, F.53, H.61, V.62, I.63, W.66, G.88, Y.89, I.98, F.106 Ligands: ACT.14 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.33, B:F.53, B:F.53, B:F.53, B:F.53, B:V.62, B:W.66, B:W.66, B:Y.89, B:I.98 Hydrogen bonds: B:Y.33, B:D.44, B:I.63, B:Y.89

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.112, V.113 Chain B: D.51, P.52 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.51, B:P.52, A:D.112, H2O.4, H2O.4 CA.8: 4 residues within 4Å: Chain A: D.51, P.52 Chain B: D.112, V.113 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.112, B:V.113, A:P.52, H2O.1, H2O.1

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: T.28 Chain B: T.28, A.54, F.55, V.56 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.54 EDO.4: 5 residues within 4Å: Chain A: T.2, V.4, Y.12, E.13, D.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.2, A:D.14 EDO.5: 3 residues within 4Å: Chain A: S.1, V.3, E.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.13 EDO.9: 5 residues within 4Å: Chain A: T.28, A.54, V.56 Chain B: T.28 Ligands: EDO.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.28 Water bridges: A:V.56 EDO.10: 5 residues within 4Å: Chain B: T.2, V.4, Y.12, E.13, D.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.2, B:T.2, B:D.14, B:D.14 EDO.11: 8 residues within 4Å: Chain A: S.30, P.52, L.111, D.112 Chain B: S.30, P.52, L.111, D.112 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.30, A:S.30 Water bridges: B:S.30, A:D.112

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: Y.33, T.34, E.107, E.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.34 ACT.12: 4 residues within 4Å: Chain B: H.32, Y.33, T.34, E.107 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.107 ACT.13: 2 residues within 4Å: Chain B: T.38, D.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.38, B:T.38 ACT.14: 5 residues within 4Å: Chain B: Q.86, G.88, Y.89, G.90 Ligands: FK5.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.88, B:A.91 ACT.15: 2 residues within 4Å: Chain B: T.5, K.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.5 Water bridges: B:T.5, B:K.11, B:K.11 Salt bridges: B:K.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begley, D.W. et al., A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Antimicrob.Agents Chemother. (2014)

Release Date

2012-03-28

Peptides

Peptidyl-prolyl cis-trans isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidyl-prolyl cis-trans isomerase