SMTL ID : 4ryu.1 (1 other biounit)

Crystal Structure of C2 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: G.54, P.109, N.110, D.114, S.118 Chain B: L.61 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.54, A:P.109, A:N.110, A:N.110 Water bridges: A:N.106, A:N.106, A:G.119 PO4.2: 7 residues within 4Å: Chain A: A.196, I.213, G.214, P.215, P.216 Chain B: L.59, Y.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.214 Water bridges: A:A.196, A:G.217 PO4.3: 5 residues within 4Å: Chain A: Y.87, A.126, R.128 Chain B: Y.117, A.196 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.126, A:R.128, B:Y.117, B:A.196 Water bridges: A:N.91, A:R.128, B:Y.117 PO4.4: 2 residues within 4Å: Chain A: Y.220, D.221 No protein-ligand interaction detected (PLIP) PO4.5: 6 residues within 4Å: Chain A: V.25, H.26, Q.31, F.70, N.72, D.74 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.72, A:D.74 Water bridges: A:H.26, A:N.72, A:N.72 Salt bridges: A:H.26 PO4.7: 7 residues within 4Å: Chain A: L.61 Chain B: P.109, N.110, D.114, Y.117, S.118 Ligands: MPD.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.54, B:N.110, B:N.110 Water bridges: B:N.106, B:N.106, B:G.119

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.22, D.23, S.53, N.106 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.22, A:D.23, A:S.53, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.22, D.23, S.53, N.106 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.22, B:D.23, B:S.53, H2O.12, H2O.12

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: L.61 Chain B: I.213, G.214, P.215 Ligands: MPD.11 2 PLIP interactions: 2 interactions with chain B Water bridges: B:I.213, B:G.214

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 1 residues within 4Å: Chain B: R.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.206 MPD.11: 9 residues within 4Å: Chain A: L.61 Chain B: D.114, Y.117, A.196, I.213, G.214, P.216 Ligands: PO4.7, GOL.9 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.114, B:Y.117, B:A.196, B:P.216, A:L.61 Hydrogen bonds: B:G.214 Water bridges: B:D.114 MPD.12: 7 residues within 4Å: Chain A: Y.117, A.196 Chain B: Y.87, V.90, N.91, A.126, R.128 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.87, B:Y.87, B:V.90, A:A.196 Hydrogen bonds: B:N.91, A:Y.117, A:A.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathiharan, Y.K. et al., Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Acta Crystallogr. D Biol. Crystallogr. (2015)

Release Date

2015-09-09

Peptides

5'/3'-nucleotidase SurE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'/3'-nucleotidase SurE

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