SMTL ID : 3owf.1

Crystal structure of Staphylococcal nuclease variant Delta+PHS V66R at cryogenic temperature

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x THP: THYMIDINE-3',5'-DIPHOSPHATE(Non-covalent)

THP.1: 12 residues within 4Å: Chain A: D.21, R.35, L.36, D.40, D.77, K.78, Y.79, R.81, L.83, Y.107, Y.109 Ligands: CA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.35, A:Y.107, A:Y.107 Hydrogen bonds: A:D.21, A:Y.79, A:R.81 Water bridges: A:K.78, A:K.78 Salt bridges: A:R.35, A:K.78, A:R.81 THP.4: 12 residues within 4Å: Chain B: D.21, R.35, L.36, D.40, D.77, K.78, Y.79, R.81, L.83, Y.107, Y.109 Ligands: CA.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.35, B:Y.107, B:Y.107 Hydrogen bonds: B:D.21, B:R.81 Water bridges: B:D.19, B:K.78, B:K.78 Salt bridges: B:R.35, B:K.78, B:R.81

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.21, R.35, D.40, T.41 Ligands: THP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.21, A:D.40, A:T.41, H2O.1, H2O.1 CA.5: 5 residues within 4Å: Chain B: D.21, R.35, D.40, T.41 Ligands: THP.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.21, B:D.40, B:T.41, H2O.5, H2O.5

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

PO4.3: 7 residues within 4Å: Chain A: K.57, R.60, E.61 Chain B: K.57, R.60, E.61 Ligands: PO4.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.57, B:R.60, A:K.57, A:R.60 PO4.6: 7 residues within 4Å: Chain A: K.57, R.60, E.61 Chain B: K.57, R.60, E.61 Ligands: PO4.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.57, B:R.60, A:K.57, A:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schlessman, J.L. et al., Domain swapping promoted by a single mutation that introduces an ionizable group into the hydrophobic core of a protein. To be Published

Release Date

2010-10-20

Peptides

Thermonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thermonuclease