SMTL ID : 4r8n.1

Crystal structure of Staphylococcal nuclease variant V23I/V66I/I72V/I92V 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: 12 residues within 4Å: Chain A: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.35, A:L.89, A:Y.113, A:Y.113 Hydrogen bonds: A:D.83 Water bridges: A:T.22, A:T.22, A:E.43, A:Y.113 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.2, H2O.2

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

PO4.3: 3 residues within 4Å: Chain A: Y.27, F.76, T.82 No protein-ligand interaction detected (PLIP)

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 3 residues within 4Å: Chain A: F.61, K.64, M.65 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.61, A:K.64, A:M.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caro, J.A. et al., Cavities in proteins. To be Published

Release Date

2014-09-17

Peptides

Thermonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thermonuclease