SMTL ID : 2qjv.1

Crystal structure of an iolb-like protein (stm4420) from salmonella typhimurium lt2 at 1.90 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

12 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: H.91, H.92 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.91, A:H.92, H2O.7, H2O.8, H2O.8 NI.2: 4 residues within 4Å: Chain A: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.171, A:H.173, A:E.186, A:H.229, H2O.1, H2O.1 NI.10: 2 residues within 4Å: Chain B: H.91, H.92 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.91, B:H.92, H2O.22, H2O.23, H2O.24 NI.11: 4 residues within 4Å: Chain B: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.171, B:H.173, B:E.186, B:H.229, H2O.15, H2O.16 NI.18: 2 residues within 4Å: Chain C: H.91, H.92 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.91, C:H.92, H2O.35, H2O.36, H2O.36 NI.19: 4 residues within 4Å: Chain C: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.171, C:H.173, C:E.186, C:H.229, H2O.29, H2O.29 NI.27: 2 residues within 4Å: Chain D: H.91, H.92 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.91, D:H.92, H2O.49, H2O.50, H2O.52 NI.28: 4 residues within 4Å: Chain D: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.171, D:H.173, D:E.186, D:H.229, H2O.43, H2O.43 NI.35: 2 residues within 4Å: Chain E: H.91, H.92 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.91, E:H.92, H2O.63, H2O.64, H2O.64 NI.36: 4 residues within 4Å: Chain E: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.171, E:H.173, E:E.186, E:H.229, H2O.57, H2O.57 NI.44: 2 residues within 4Å: Chain F: H.91, H.92 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.91, F:H.92, H2O.77, H2O.78, H2O.80 NI.45: 4 residues within 4Å: Chain F: H.171, H.173, E.186, H.229 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.171, F:H.173, F:E.186, F:H.229, H2O.71, H2O.71

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

CL.3: 3 residues within 4Å: Chain A: G.179, L.249, R.253 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: Y.85 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.138, S.167 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: A.65, D.66, S.67 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: D.47, E.48 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: R.131, R.138, S.166, S.167, Y.241 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: E.178, G.179, R.253 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: G.179, L.249, R.253 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain C: Y.85 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: R.138, S.167 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: A.65, D.66, S.67 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain D: D.47, E.48 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain D: R.131, R.138, S.166, S.167, Y.241 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain D: E.178, G.179, R.253 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain E: G.179, L.249, R.253 Ligand excluded by PLIP CL.38: 1 residues within 4Å: Chain E: Y.85 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain E: R.138, S.167 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain E: A.65, D.66, S.67 Ligand excluded by PLIP CL.46: 2 residues within 4Å: Chain F: D.47, E.48 Ligand excluded by PLIP CL.47: 5 residues within 4Å: Chain F: R.131, R.138, S.166, S.167, Y.241 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain F: E.178, G.179, R.253 Ligand excluded by PLIP

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

SO4.7: 2 residues within 4Å: Chain A: R.81, H.130 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.81 Salt bridges: A:R.81, A:H.130 SO4.8: 4 residues within 4Å: Chain A: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.218 Water bridges: A:E.104, A:R.191, A:R.191, A:R.191, A:R.219 Salt bridges: A:R.191, A:R.219 SO4.15: 3 residues within 4Å: Chain B: R.81, H.130, L.139 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.81 Salt bridges: B:R.81, B:H.130 SO4.16: 4 residues within 4Å: Chain B: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.218 Water bridges: B:R.191, B:R.191, B:R.191, B:R.219, B:R.219 Salt bridges: B:R.191, B:R.219 SO4.24: 2 residues within 4Å: Chain C: R.81, H.130 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.81 Salt bridges: C:R.81, C:H.130 SO4.25: 4 residues within 4Å: Chain C: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.218 Water bridges: C:E.104, C:R.191, C:R.191, C:R.191, C:R.219 Salt bridges: C:R.191, C:R.219 SO4.32: 3 residues within 4Å: Chain D: R.81, H.130, L.139 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.81 Salt bridges: D:R.81, D:H.130 SO4.33: 4 residues within 4Å: Chain D: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.218 Water bridges: D:R.191, D:R.191, D:R.191, D:R.219, D:R.219 Salt bridges: D:R.191, D:R.219 SO4.41: 2 residues within 4Å: Chain E: R.81, H.130 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.81 Salt bridges: E:R.81, E:H.130 SO4.42: 4 residues within 4Å: Chain E: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:N.218 Water bridges: E:E.104, E:R.191, E:R.191, E:R.191, E:R.219 Salt bridges: E:R.191, E:R.219 SO4.49: 3 residues within 4Å: Chain F: R.81, H.130, L.139 3 PLIP interactions: 3 interactions with chain F Water bridges: F:R.81 Salt bridges: F:R.81, F:H.130 SO4.50: 4 residues within 4Å: Chain F: R.191, P.195, N.218, R.219 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.218 Water bridges: F:R.191, F:R.191, F:R.191, F:R.219, F:R.219 Salt bridges: F:R.191, F:R.219

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: K.63, E.94, A.95, K.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.94 Water bridges: A:A.65 GOL.17: 6 residues within 4Å: Chain B: S.61, K.63, F.68, Y.70, K.96, T.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.61, B:T.98 Water bridges: B:T.98 GOL.26: 4 residues within 4Å: Chain C: K.63, E.94, A.95, K.96 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.94, C:E.94 Water bridges: C:A.65 GOL.34: 6 residues within 4Å: Chain D: S.61, K.63, F.68, Y.70, K.96, T.98 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.61, D:Y.70, D:T.98 Water bridges: D:T.98 GOL.43: 4 residues within 4Å: Chain E: K.63, E.94, A.95, K.96 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.94, E:E.94 Water bridges: E:A.65 GOL.51: 6 residues within 4Å: Chain F: S.61, K.63, F.68, Y.70, K.96, T.98 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.61, F:T.98, F:T.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of uncharacterized IolB-like protein (16422983) from Salmonella typhimurium LT2 at 1.90 A resolution. To be published

Release Date

2007-08-07

Peptides

Uncharacterized IolB-like protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uncharacterized IolB-like protein