SMTL ID : 3bq9.1

Crystal structure of predicted nucleotide-binding protein from Idiomarina baltica OS145

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: G.152, G.153, H.154, E.220, G.254, G.255, A.256, G.257, T.258 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.152, A:H.154, A:G.255, A:G.257, A:T.258, A:T.258 Water bridges: A:S.155, A:E.220, A:A.256, A:A.256 Salt bridges: A:H.154 SO4.5: 9 residues within 4Å: Chain B: G.152, G.153, H.154, E.220, G.254, G.255, A.256, G.257, T.258 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.154, B:G.255, B:G.257, B:T.258 Water bridges: B:S.155, B:E.220, B:A.256 Salt bridges: B:H.154 SO4.10: 9 residues within 4Å: Chain C: G.152, G.153, H.154, E.220, G.254, G.255, A.256, G.257, T.258 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.152, C:H.154, C:G.255, C:G.257, C:T.258, C:T.258 Water bridges: C:S.155, C:E.220, C:A.256, C:A.256 Salt bridges: C:H.154 SO4.14: 9 residues within 4Å: Chain D: G.152, G.153, H.154, E.220, G.254, G.255, A.256, G.257, T.258 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.154, D:G.255, D:G.257, D:T.258 Water bridges: D:S.155, D:E.220, D:A.256 Salt bridges: D:H.154

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: S.16, Q.17, L.18, R.68 Chain D: H.127, W.348 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.17, A:L.18, A:R.68, D:H.127 Water bridges: A:R.68 GOL.3: 9 residues within 4Å: Chain A: L.34, D.104, I.105, T.108, I.132, P.214, I.231, L.232, P.233 No protein-ligand interaction detected (PLIP) GOL.4: 8 residues within 4Å: Chain A: E.160, S.288, S.289, R.290, D.291, Y.292, Q.433, R.435 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.160, A:E.160, A:S.289, A:D.291, A:Y.292, A:R.435 Water bridges: A:N.157, A:R.290, A:Q.433 GOL.6: 6 residues within 4Å: Chain B: S.11, M.12, L.15, L.102, R.103, L.106 6 PLIP interactions: 6 interactions with chain B Water bridges: B:S.11, B:S.11, B:S.11, B:S.11, B:R.103, B:R.103 GOL.7: 6 residues within 4Å: Chain B: S.16, Q.17, L.18, R.68 Chain C: H.127, W.348 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.17, B:L.18, C:H.127 Water bridges: C:W.348 GOL.8: 3 residues within 4Å: Chain B: A.25, S.26, S.27 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.26, B:S.26, B:S.27, B:S.27 Water bridges: B:K.24 GOL.9: 8 residues within 4Å: Chain B: I.216, I.235, R.238, L.239, F.242, G.257, E.260, E.261 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.238, B:R.238, B:E.261, B:E.261 Water bridges: B:E.220 GOL.11: 6 residues within 4Å: Chain B: H.127, W.348 Chain C: S.16, Q.17, L.18, R.68 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.17, C:L.18, C:R.68, B:H.127 Water bridges: C:R.68 GOL.12: 9 residues within 4Å: Chain C: L.34, D.104, I.105, T.108, I.132, P.214, I.231, L.232, P.233 No protein-ligand interaction detected (PLIP) GOL.13: 8 residues within 4Å: Chain C: E.160, S.288, S.289, R.290, D.291, Y.292, Q.433, R.435 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.160, C:E.160, C:S.289, C:D.291, C:Y.292, C:R.435 Water bridges: C:N.157, C:R.290, C:Q.433 GOL.15: 6 residues within 4Å: Chain D: S.11, M.12, L.15, L.102, R.103, L.106 6 PLIP interactions: 6 interactions with chain D Water bridges: D:S.11, D:S.11, D:S.11, D:S.11, D:R.103, D:R.103 GOL.16: 6 residues within 4Å: Chain A: H.127, W.348 Chain D: S.16, Q.17, L.18, R.68 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.17, D:L.18, A:H.127 Water bridges: A:W.348 GOL.17: 3 residues within 4Å: Chain D: A.25, S.26, S.27 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.26, D:S.26, D:S.27, D:S.27 Water bridges: D:K.24 GOL.18: 8 residues within 4Å: Chain D: I.216, I.235, R.238, L.239, F.242, G.257, E.260, E.261 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.238, D:R.238, D:E.261, D:E.261 Water bridges: D:E.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Predicted Nucleotide-Binding Protein from Idiomarina baltica. To be Published

Release Date

2008-01-01

Peptides

Predicted Rossmann fold nucleotide-binding domain-containing protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Predicted Rossmann fold nucleotide-binding domain-containing protein