SMTL ID : 4qf4.1 (2 other biounits)

Crystal structure of Staphylococcal nuclease variant V23M at cryogenic temperature

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

THP.1: 13 residues within 4Å: Chain A: D.21, 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:Y.113, A:Y.113 Hydrogen bonds: A:Y.85, A:R.87 Water bridges: A:T.22, A:T.22, A:E.43, A:Y.115 Salt bridges: A:R.35, A:K.84, A:R.87 THP.4: 13 residues within 4Å: Chain B: D.21, R.35, L.36, L.37, D.40, D.83, K.84, Y.85, R.87, L.89, Y.113, Y.115 Ligands: CA.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.35, B:L.89, B:Y.113, B:Y.113 Hydrogen bonds: B:Y.85, B:R.87 Water bridges: B:T.22, B:T.22, B:E.43 Salt bridges: B:R.35, B:K.84, B:R.87

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.2 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.3, H2O.3

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

PO4.3: 5 residues within 4Å: Chain A: Y.27, M.32, F.76, R.81, T.82 No protein-ligand interaction detected (PLIP) PO4.6: 5 residues within 4Å: Chain A: K.134, E.135 Chain B: Y.27, F.76, T.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2014-06-04

Peptides

Thermonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thermonuclease

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