SMTL ID : 7qr1.1

SpCas9 bound to TRAC off-target2 DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Chain A: U.24 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: U.52 No protein-ligand interaction detected (PLIP)

14 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.3: 3 residues within 4Å: Chain A: A.67, U.68 Chain B: T.1102 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.1102, H2O.5 K.4: 2 residues within 4Å: Chain A: A.70 Chain B: Q.1350 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.1350, H2O.1, H2O.2 K.5: 1 residues within 4Å: Chain A: G.23 No protein-ligand interaction detected (PLIP) K.6: 2 residues within 4Å: Chain A: U.68 Chain B: R.1171 No protein-ligand interaction detected (PLIP) K.7: 4 residues within 4Å: Chain A: C.10, U.11 Chain C: G.19, T.20 No protein-ligand interaction detected (PLIP) K.8: 4 residues within 4Å: Chain A: G.17, G.18 Chain B: R.63, L.64 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain A: A.28, G.29, U.47 No protein-ligand interaction detected (PLIP) K.10: 5 residues within 4Å: Chain B: L.623, T.624, F.626, Y.656 Chain C: G.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.626, B:Y.656, H2O.8 K.11: 5 residues within 4Å: Chain B: G.361, Y.362, G.365, A.367, K.401 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Y.362 K.12: 2 residues within 4Å: Chain B: A.640, F.643 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:F.643, H2O.10 K.13: 4 residues within 4Å: Chain B: I.226, L.229, P.230, E.232 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.229, B:E.232, H2O.8 K.14: 2 residues within 4Å: Chain B: E.108, K.111 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.111, H2O.9, H2O.10 K.15: 3 residues within 4Å: Chain B: E.584, R.586, N.588 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.584, B:R.586, H2O.11, H2O.12 K.16: 4 residues within 4Å: Chain B: E.381, M.383, T.386, L.390 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pacesa, M. et al., Structural basis for Cas9 off-target activity. Cell (2022)

Release Date

2022-10-26

Peptides

CRISPR-associated endonuclease Cas9/Csn1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

CRISPR-associated endonuclease Cas9/Csn1

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