SMTL ID : 6m0x.1

Crystal structure of Streptococcus thermophilus Cas9 in complex with AGGA PAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

monomer

Ligands

1 x DA- DA- DA- DG- DG- DA- DG- DC: DNA (5'-D(*AP*AP*AP*GP*GP*AP*GP*C)-3')(Non-covalent)

DA-DA-DA-DG-DG-DA-DG-DC.1: 27 residues within 4Å: Chain A: F.674, K.868, S.941, K.942, G.944, N.945, S.962, V.963, P.965, K.985, K.1026, L.1046, S.1047, M.1050, P.1051, E.1058, K.1060, Q.1085, K.1087 Chain C: G.1, C.2, T.3, C.4, C.5, T.6, T.7, T.8 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.1056, A:A.1081 Hydrogen bonds: A:S.605, A:Q.628, A:A.826, A:T.827, A:T.827, A:Q.1053, A:N.1079, A:N.1082, A:S.1083, A:Q.1085 Salt bridges: A:K.864, A:K.1088 pi-Stacking: A:F.674

14 x BA: BARIUM ION(Non-covalent)(Non-functional Binders)

BA.2: 2 residues within 4Å: Chain A: G.422 Chain C: T.17 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.422 BA.3: 1 residues within 4Å: Chain A: K.849 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.849 BA.4: 2 residues within 4Å: Chain A: T.515, N.516 No protein-ligand interaction detected (PLIP) BA.5: 2 residues within 4Å: Chain A: D.825, S.962 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.825, H2O.1 BA.6: 1 residues within 4Å: Chain A: D.169 No protein-ligand interaction detected (PLIP) BA.7: 4 residues within 4Å: Chain A: K.358, L.360, L.363, D.364 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:K.358, A:L.360 BA.10: 2 residues within 4Å: Chain B: U.51, G.54 No protein-ligand interaction detected (PLIP) BA.11: 1 residues within 4Å: Chain B: G.41 No protein-ligand interaction detected (PLIP) BA.12: 1 residues within 4Å: Chain B: U.3 No protein-ligand interaction detected (PLIP) BA.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.14: 1 residues within 4Å: Chain B: G.34 No protein-ligand interaction detected (PLIP) BA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.16: 1 residues within 4Å: Chain C: G.1 No protein-ligand interaction detected (PLIP) BA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain A: D.599, A.600, N.623 Chain C: C.11, C.12 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.599, H2O.1, H2O.1 MG.9: 2 residues within 4Å: Chain A: S.1083, G.1084 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.1083

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Catalytic-state structure and engineering of Streptococcus thermophilus Cas9. Nat Catal (2020)

Release Date

2020-09-09

Peptides

CRISPR-associated endonuclease Cas9 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CRISPR-associated endonuclease Cas9 1

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