SMTL ID : 4k6d.1

Crystal structure of Staphylococcal nuclease variant V23M/T62F at cryogenic temperature

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

THP.1: 13 residues within 4Å: Chain A: T.22, R.35, L.36, L.37, D.40, D.83, K.84, Y.85, R.87, L.89, Y.113, Y.115 Ligands: CA.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.35, A:Y.113, A:Y.113 Hydrogen bonds: A:T.22, A:Y.85, A:R.87, A:Y.113 Water bridges: A:T.22 Salt bridges: A:R.35, A:K.84, A:R.87

1 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.3, H2O.3

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

MPD.3: 3 residues within 4Å: Chain A: L.14, I.15, E.67 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.14, A:E.67 Hydrogen bonds: A:E.67 MPD.5: 4 residues within 4Å: Chain A: F.61, K.64, M.65, K.97 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.61, A:M.65

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

PO4.4: 1 residues within 4Å: Chain A: K.134 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caro, J.A. et al., Pressure effects on proteins. To be Published

Release Date

2013-04-24

Peptides

Thermonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermonuclease