SMTL ID : 3e49.1

Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.50, H.52, R.255, E.259 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.50, A:H.52, A:E.259, H2O.1, H2O.1 ZN.3: 4 residues within 4Å: Chain B: H.50, H.52, R.255, E.259 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.50, B:H.52, B:E.259, H2O.9, H2O.9 ZN.9: 3 residues within 4Å: Chain C: H.50, H.52, E.259 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.50, C:H.52, C:E.259, H2O.17, H2O.26 ZN.15: 3 residues within 4Å: Chain D: H.50, H.52, E.259 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.50, D:H.52, D:E.259, H2O.26, H2O.26

7 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.2: 6 residues within 4Å: Chain A: R.218, G.226, A.227, Y.229, W.231, Q.250 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.231 Water bridges: A:A.227 ETX.4: 6 residues within 4Å: Chain B: R.218, G.226, A.227, Y.229, W.231, Q.250 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.229 Hydrogen bonds: B:R.218 Water bridges: B:W.231 ETX.5: 3 residues within 4Å: Chain B: S.5, V.230, M.300 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.230 Hydrogen bonds: B:S.5 Water bridges: B:G.251, B:N.253 ETX.6: 2 residues within 4Å: Chain B: E.70, R.74 No protein-ligand interaction detected (PLIP) ETX.10: 5 residues within 4Å: Chain C: R.218, G.226, Y.229, W.231, Q.250 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.229 Hydrogen bonds: C:Q.250 Water bridges: C:R.218 ETX.11: 5 residues within 4Å: Chain C: D.222, R.223, F.225, G.226, D.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.228 Water bridges: C:A.227, C:D.228 ETX.12: 5 residues within 4Å: Chain C: R.238, W.263, A.265, P.266, G.267 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.263

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

ACT.7: 2 residues within 4Å: Chain B: G.164, N.165 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.165 ACT.13: 3 residues within 4Å: Chain C: E.96, E.97, R.100 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.96 Water bridges: C:E.96 Salt bridges: C:R.100

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 8 residues within 4Å: Chain A: Y.180 Chain B: G.202, L.203, L.204, G.206, I.207, G.208, P.209 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.205 IMD.14: 7 residues within 4Å: Chain C: G.202, L.203, L.204, G.206, I.207, G.208 Chain D: Y.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.206 Water bridges: C:G.205 IMD.16: 6 residues within 4Å: Chain D: R.218, D.222, Y.229, W.231, Q.250, G.251 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.222 IMD.17: 7 residues within 4Å: Chain C: Y.180 Chain D: G.202, L.203, L.204, G.206, I.207, G.208 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.202, D:G.205 IMD.18: 4 residues within 4Å: Chain D: R.238, W.263, A.265, P.266 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_556190.1) from BURKHOLDERIA XENOVORANS LB400 at 1.75 A resolution. To be published

Release Date

2008-08-26

Peptides

uncharacterized protein DUF849 with a TIM barrel fold: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

uncharacterized protein DUF849 with a TIM barrel fold