SMTL ID : 5fw1.1

Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

K.1: 3 residues within 4Å: Chain A: U.14, G.15 Chain C: C.16 No protein-ligand interaction detected (PLIP) K.2: 4 residues within 4Å: Chain A: U.24, U.25 Chain B: G.369, G.370 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.369 K.5: 4 residues within 4Å: Chain A: A.70 Chain B: T.1102, Q.1354, S.1355 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.1354, H2O.4 K.6: 3 residues within 4Å: Chain B: E.588, R.590, N.592 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.588, B:R.590, H2O.8 K.7: 3 residues within 4Å: Chain A: A.67, U.68 Chain B: T.1106 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.1106, H2O.4 K.8: 7 residues within 4Å: Chain B: L.627, T.628, F.630, E.631, R.659, Y.660, T.661 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:L.627, B:T.628, B:Y.660 K.9: 6 residues within 4Å: Chain B: G.365, Y.366, G.369, G.370, A.371, K.405 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.366, B:G.369, B:A.371 K.10: 5 residues within 4Å: Chain B: I.230, L.233, P.234, G.235, E.236 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.230, B:L.233, B:E.236, H2O.6 K.11: 2 residues within 4Å: Chain B: E.112, K.115 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.115, H2O.5, H2O.5 K.12: 4 residues within 4Å: Chain B: A.644, H.645, F.647, D.648 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:F.647 K.13: 1 residues within 4Å: Chain B: E.61 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.61, H2O.5 K.14: 3 residues within 4Å: Chain A: G.23 Chain B: R.407 Ligands: MG.3 No protein-ligand interaction detected (PLIP) K.15: 3 residues within 4Å: Chain C: A.8 Chain D: A.4, T.5 No protein-ligand interaction detected (PLIP)

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

MG.3: 2 residues within 4Å: Chain A: G.23 Ligands: K.14 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: U.52, G.64 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anders, C. et al., Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol.Cell (2016)

Release Date

2016-04-20

Peptides

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1