SMTL ID : 7qqr.1

SpCas9 bound to AAVS1 off-target5 DNA substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: U.52, G.64 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

K.3: 5 residues within 4Å: Chain A: G.5, G.6, C.7 Chain C: G.24, T.25 No protein-ligand interaction detected (PLIP) K.4: 3 residues within 4Å: Chain A: A.67, U.68 Chain B: T.1102 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.1102, H2O.2, H2O.6 K.5: 2 residues within 4Å: Chain A: A.70 Chain B: Q.1350 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.1350, H2O.3 K.6: 1 residues within 4Å: Chain A: G.29 No protein-ligand interaction detected (PLIP) K.7: 2 residues within 4Å: Chain A: G.14, G.15 No protein-ligand interaction detected (PLIP) K.10: 1 residues within 4Å: Chain B: E.57 No protein-ligand interaction detected (PLIP) K.11: 5 residues within 4Å: Chain B: L.623, T.624, F.626, Y.656 Chain C: C.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.624, B:Y.656 K.12: 5 residues within 4Å: Chain B: G.361, Y.362, G.365, A.367, K.401 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.365, B:A.367 K.13: 3 residues within 4Å: Chain B: A.640, F.643, D.645 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.640, B:F.643 K.14: 3 residues within 4Å: Chain B: I.226, L.229, E.232 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.226, B:L.229, B:E.232 K.15: 3 residues within 4Å: Chain B: E.108, K.111, H.113 No protein-ligand interaction detected (PLIP) K.16: 3 residues within 4Å: Chain B: E.584, R.586, N.588 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.584, B:R.586, H2O.7, H2O.8, H2O.9 K.19: 3 residues within 4Å: Chain A: C.17 Chain C: T.13, G.14 No protein-ligand interaction detected (PLIP)

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

EDO.8: 2 residues within 4Å: Chain A: G.4, G.5 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: G.60, U.61 Chain B: N.77 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.77 EDO.17: 6 residues within 4Å: Chain A: A.53 Chain B: F.1105, S.1106, K.1107, E.1108, F.1134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.1105, B:S.1106 EDO.18: 4 residues within 4Å: Chain A: G.64, U.65, U.66 Chain B: R.461 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.461 EDO.20: 4 residues within 4Å: Chain A: U.22, G.23 Chain C: G.9, G.10 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

Related Entries With Identical Sequence