SMTL ID : 4wgf.1

YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-octamer

Ligands

8 x ROP: PROPIONAMIDE(Covalent)

ROP.1: 8 residues within 4Å: Chain A: D.19, S.59, N.65, I.88, V.113, V.114, C.118 Chain B: W.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.59, A:S.59, A:N.65 ROP.6: 10 residues within 4Å: Chain B: D.19, L.24, S.59, N.65, R.84, I.88, V.113, V.114, C.118 Chain C: W.176 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.24 Hydrogen bonds: B:D.19, B:S.59, B:S.59, B:N.65, B:R.84 ROP.10: 9 residues within 4Å: Chain C: D.19, S.59, N.65, R.84, I.88, V.113, V.114, C.118 Chain D: W.176 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.19, C:S.59, C:S.59, C:N.65, C:R.84 ROP.14: 8 residues within 4Å: Chain A: W.176 Chain D: D.19, S.59, N.65, I.88, V.113, V.114, C.118 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.59, D:S.59, D:N.65, D:R.84 ROP.18: 8 residues within 4Å: Chain E: D.19, S.59, N.65, I.88, V.113, V.114, C.118 Chain F: W.176 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.59, E:S.59, E:N.65, E:R.84 ROP.21: 8 residues within 4Å: Chain F: D.19, S.59, N.65, I.88, V.113, V.114, C.118 Chain G: W.176 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.59, F:S.59, F:N.65 ROP.26: 9 residues within 4Å: Chain G: D.19, S.59, N.65, R.84, I.88, V.113, V.114, C.118 Chain H: W.176 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:D.19, G:S.59, G:S.59, G:N.65, G:R.84 ROP.30: 8 residues within 4Å: Chain E: W.176 Chain H: D.19, S.59, N.65, I.88, V.113, V.114, C.118 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:D.19, H:D.19, H:S.59, H:N.65

8 x HX2: (2R,5R)-hexane-2,5-diol(Non-covalent)(Covalent)

HX2.2: 8 residues within 4Å: Chain A: P.192, A.195, N.196 Chain E: L.25, K.37, V.40, V.69, E.71 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Water bridges: A:G.188, A:L.191 Hydrophobic interactions: E:L.25, E:V.69 HX2.5: 9 residues within 4Å: Chain A: L.25, P.33, K.37, V.40, L.41, V.69, E.71 Chain E: P.192, N.196 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:L.25, A:K.37, A:K.37, A:L.41, A:V.69, A:V.69, A:E.71, E:P.192 Hydrogen bonds: E:N.196, E:N.196 HX2.7: 8 residues within 4Å: Chain B: P.192, A.193, A.195, N.196 Chain H: L.25, K.37, V.69, E.71 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain H Hydrophobic interactions: B:A.195, H:K.37, H:V.69 Hydrogen bonds: B:N.196 HX2.11: 9 residues within 4Å: Chain C: P.192, A.195, N.196 Chain G: L.25, K.37, V.40, L.41, V.69, E.71 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain C Hydrophobic interactions: G:L.25, G:K.37, G:V.69, C:P.192 Hydrogen bonds: C:N.196, C:N.196 HX2.15: 7 residues within 4Å: Chain D: P.192, N.196 Chain F: L.25, K.37, V.40, L.41, V.69 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.25, F:K.37, F:V.40, F:V.69 Hydrogen bonds: F:E.71, D:P.192, D:N.196 HX2.22: 8 residues within 4Å: Chain D: L.25, K.37, V.40, L.41, V.69, E.71 Chain F: P.192, N.196 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:L.25, D:K.37, D:V.40, D:V.69 Hydrogen bonds: F:N.196 HX2.27: 8 residues within 4Å: Chain C: L.25, K.37, V.40, L.41, V.69, E.71 Chain G: P.192, N.196 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:L.25, C:K.37, C:V.40, C:L.41, C:V.69 Hydrogen bonds: C:E.71, G:N.196 Water bridges: C:P.33 HX2.31: 8 residues within 4Å: Chain B: L.25, K.37, V.40, L.41, V.69 Chain H: P.192, A.195, N.196 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain B Hydrophobic interactions: H:P.192, H:A.195, B:K.37, B:V.69 Hydrogen bonds: H:N.196

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain C: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain A: R.177 Chain D: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain E: R.84, P.85, G.86, N.87, N.93 Chain F: R.177 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain F: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain G: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain H: R.84, P.85, G.86, N.87, N.93 Ligand excluded by PLIP

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

SO4.4: 2 residues within 4Å: Chain A: R.7, R.174 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.7, A:R.174 SO4.9: 2 residues within 4Å: Chain B: R.7, R.174 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.174, B:R.174, B:R.174, B:R.174 Salt bridges: B:R.7, B:R.174 SO4.13: 2 residues within 4Å: Chain C: R.7, R.174 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.174, C:R.174 Salt bridges: C:R.7, C:R.174 SO4.17: 2 residues within 4Å: Chain D: R.7, R.174 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Water bridges: D:R.7, D:R.7, D:R.174, C:D.92 Salt bridges: D:R.7, D:R.174 SO4.20: 2 residues within 4Å: Chain E: R.7, R.174 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.7, E:R.174 SO4.24: 2 residues within 4Å: Chain F: R.7, R.174 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.7, F:R.174 SO4.25: 1 residues within 4Å: Chain F: R.48 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.48 SO4.29: 2 residues within 4Å: Chain G: R.7, R.174 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:R.7, G:R.174 SO4.33: 2 residues within 4Å: Chain H: R.7, R.174 8 PLIP interactions: 8 interactions with chain H Water bridges: H:R.7, H:R.7, H:R.7, H:R.174, H:R.174, H:R.174 Salt bridges: H:R.7, H:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grftehauge, M.K. et al., Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct. Int J Mol Sci (2015)

Release Date

2015-07-29

Peptides

Probable hydrolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Probable hydrolase

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