SMTL ID : 6m0v.1

Crsytal structure of streptococcus thermophilus Cas9 in complex with the GGAA PAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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

DA-DA-DG-DG-DA-DA-DG-DC.1: 26 residues within 4Å: Chain B: G.1, C.2, T.3, T.4, C.5, C.6, T.7, T.8 Chain C: F.674, K.868, K.942, G.944, N.945, S.962, V.963, P.965, K.985, K.1026, L.1046, S.1047, T.1049, M.1050, E.1058, K.1060, Q.1085, K.1087 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.1056 Hydrogen bonds: C:S.605, C:Q.628, C:A.826, C:T.827, C:T.827, C:Q.1053, C:N.1082, C:N.1082, C:Q.1085, C:Q.1085 Salt bridges: C:K.673, C:K.864, C:K.864, C:K.1088, C:K.1092 pi-Stacking: C:F.674

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

BA.2: 2 residues within 4Å: Chain A: U.51, G.54 No protein-ligand interaction detected (PLIP) BA.3: 1 residues within 4Å: Chain A: G.41 No protein-ligand interaction detected (PLIP) BA.4: 1 residues within 4Å: Chain A: U.3 No protein-ligand interaction detected (PLIP) BA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.6: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP) BA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) BA.8: 2 residues within 4Å: Chain B: T.17 Chain C: G.422 No protein-ligand interaction detected (PLIP) BA.9: 1 residues within 4Å: Chain C: K.849 No protein-ligand interaction detected (PLIP) BA.10: 1 residues within 4Å: Chain C: T.515 No protein-ligand interaction detected (PLIP) BA.11: 2 residues within 4Å: Chain C: D.825, S.962 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 5 residues within 4Å: Chain B: C.11, C.12 Chain C: D.599, A.600, N.623 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.599

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: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

CRISPR-associated endonuclease Cas9 1

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