SMTL ID : 4q7a.1

Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.303, T.304, G.305, S.328, D.331 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.304, A:T.304, A:G.305, A:S.328, A:D.331, A:D.331 Salt bridges: A:K.303 SO4.3: 4 residues within 4Å: Chain B: K.303, T.304, G.305, S.328 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.304, B:T.304, B:G.305, B:S.328 Salt bridges: B:K.303 SO4.4: 4 residues within 4Å: Chain B: D.53, G.54, H.139, T.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.54 Water bridges: B:H.139, B:T.143 Salt bridges: B:H.139 SO4.7: 3 residues within 4Å: Chain D: H.213, A.214 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.214 Salt bridges: D:H.213 SO4.10: 5 residues within 4Å: Chain E: K.303, T.304, G.305, S.328, D.331 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:T.304, E:T.304, E:G.305, E:S.328, E:D.331, E:D.331 Salt bridges: E:K.303 SO4.12: 4 residues within 4Å: Chain F: K.303, T.304, G.305, S.328 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.304, F:T.304, F:G.305, F:S.328 Salt bridges: F:K.303 SO4.13: 4 residues within 4Å: Chain F: D.53, G.54, H.139, T.143 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.54 Water bridges: F:H.139, F:T.143 Salt bridges: F:H.139 SO4.16: 3 residues within 4Å: Chain H: H.213, A.214 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:A.214 Salt bridges: H:H.213

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.53, G.54, H.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.54 Water bridges: A:H.139 GOL.5: 7 residues within 4Å: Chain B: S.182, A.183, G.184 Chain C: A.214, R.217, E.219, T.304 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.217, C:E.219, C:T.304, B:A.183, B:G.184 GOL.6: 9 residues within 4Å: Chain A: S.182, A.183, G.184 Chain D: A.214, R.217, E.219, R.243, T.304 Ligands: SO4.7 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.217, D:E.219, D:R.243, A:A.183 GOL.8: 5 residues within 4Å: Chain D: T.14, A.16, D.17, L.340, E.344 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.17 GOL.11: 3 residues within 4Å: Chain E: D.53, G.54, H.139 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.54 Water bridges: E:H.139 GOL.14: 7 residues within 4Å: Chain F: S.182, A.183, G.184 Chain G: A.214, R.217, E.219, T.304 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:R.217, G:E.219, G:T.304, F:A.183, F:G.184 GOL.15: 9 residues within 4Å: Chain E: S.182, A.183, G.184 Chain H: A.214, R.217, E.219, R.243, T.304 Ligands: SO4.16 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:R.217, H:E.219, H:R.243, E:A.183 GOL.17: 5 residues within 4Å: Chain H: T.14, A.16, D.17, L.340, E.344 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.17

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

CL.9: 2 residues within 4Å: Chain D: D.212, H.216 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain H: D.212, H.216 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus. To be Published

Release Date

2014-07-02

Peptides

N-acetyl-ornithine/N-acetyl-lysine deacetylase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

N-acetyl-ornithine/N-acetyl-lysine deacetylase