SMTL ID : 5czz.1

Crystal structure of Staphylococcus aureus Cas9 in complex with sgRNA and target DNA (TTGAAT PAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x DT- DT- DG- DA- DA- DT- DA- DG: DNA (5'-D(*TP*TP*GP*AP*AP*TP*AP*G)-3')(Non-covalent)

DT-DT-DG-DA-DA-DT-DA-DG.1: 25 residues within 4Å: Chain A: N.888, K.889, N.891, A.892, S.911, L.912, K.913, P.914, I.985, N.988, N.989, L.992, R.994, E.996, R.1005, R.1018 Chain C: C.1, T.2, A.3, T.4, T.5, C.6, A.7, A.8 Ligands: EDO.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.1016 Hydrogen bonds: A:N.788, A:D.789, A:D.789, A:T.790, A:T.790, A:R.994, A:T.1022, A:T.1022 Water bridges: A:Y.792 Salt bridges: A:K.818, A:K.818, A:R.1015

5 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: Q.362, Y.392, T.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.362 NA.3: 4 residues within 4Å: Chain A: L.595, S.597, S.600, I.602 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.600 NA.4: 4 residues within 4Å: Chain A: E.234, M.235, M.237, H.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.239 NA.5: 2 residues within 4Å: Chain B: U.11, G.12 No protein-ligand interaction detected (PLIP) NA.8: 3 residues within 4Å: Chain A: N.888 Chain C: T.5, C.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.888 Water bridges: A:N.888

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

PO4.6: 1 residues within 4Å: Chain B: G.70 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: T.790 Chain B: G.21, U.22 Chain C: G.9 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: I.804, N.888 Ligands: DT-DT-DG-DA-DA-DT-DA-DG.1, DT-DT-DG-DA-DA-DT-DA-DG.1, DT-DT-DG-DA-DA-DT-DA-DG.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.888

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimasu, H. et al., Crystal Structure of Staphylococcus aureus Cas9. Cell (2015)

Release Date

2015-09-02

Peptides

CRISPR-associated endonuclease Cas9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CRISPR-associated endonuclease Cas9

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