SMTL ID : 5b2r.1

Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DT- DG- DA- DG- DA- DT- DT- DG: Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')(Non-covalent)

DT-DG-DA-DG-DA-DT-DT-DG.1: 22 residues within 4Å: Chain B: K.1111, R.1118, S.1120, K.1122, S.1140, K.1204, A.1219, S.1220, E.1223, Q.1225, A.1324, R.1337, Q.1339, R.1341 Chain C: C.1, A.2, A.3, T.4, C.5, T.6, C.7, A.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.1111, B:E.1112, B:S.1113, B:R.1337, B:R.1341 Water bridges: B:Q.1339 Salt bridges: B:K.1293, B:K.1338

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

K.2: 3 residues within 4Å: Chain A: A.65, U.66 Chain B: T.1106 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.1106, H2O.6, H2O.7, H2O.18 K.3: 2 residues within 4Å: Chain A: A.68 Chain B: Q.1354 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.1354, H2O.5, H2O.20, H2O.22, H2O.27 K.4: 1 residues within 4Å: Chain A: G.21 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain A: U.22 Chain B: D.368, G.369 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.369 K.10: 4 residues within 4Å: Chain B: L.627, T.628, F.630, Y.660 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.627, B:T.628, B:F.630, B:Y.660, H2O.28 K.11: 3 residues within 4Å: Chain B: E.588, R.590, N.592 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.588, B:R.590, H2O.8, H2O.22, H2O.29 K.12: 6 residues within 4Å: Chain B: G.365, Y.366, G.369, G.370, A.371, K.405 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.366, B:G.369, B:A.371, H2O.24 K.13: 4 residues within 4Å: Chain B: I.230, L.233, P.234, 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.25 K.14: 3 residues within 4Å: Chain B: E.112, E.113, K.115 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.112, B:K.115, H2O.26 K.15: 1 residues within 4Å: Chain B: E.61 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.61, H2O.4, H2O.22, H2O.24, H2O.25 K.16: 3 residues within 4Å: Chain B: A.644, H.645, F.647 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.644, B:F.647

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

MG.5: 1 residues within 4Å: Chain A: U.50 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: G.21, U.22 No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.7: 4 residues within 4Å: Chain A: G.62, U.63, U.64 Chain B: R.465 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.465 Water bridges: B:R.70, B:R.465 EDO.18: 6 residues within 4Å: Chain A: A.52 Chain B: F.1109, I.1172, M.1173, R.1175, S.1176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1173, B:R.1175, B:S.1176 Water bridges: B:S.1177 EDO.19: 4 residues within 4Å: Chain B: V.1143, G.1169, T.1171, A.1221 6 PLIP interactions: 6 interactions with chain B Water bridges: B:G.1169, B:G.1169, B:G.1169, B:E.1174, B:E.1174, B:E.1174 EDO.20: 9 residues within 4Å: Chain A: G.19, C.20 Chain B: Y.140, R.143, H.164, R.407, N.411, I.414, H.419 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.143, B:N.411

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 5 residues within 4Å: Chain A: A.65, U.66, C.67 Chain B: T.1106, R.1175 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.1175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, S. et al., Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Mol.Cell (2016)

Release Date

2016-03-23

Peptides

CRISPR-associated endonuclease Cas9: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

CRISPR-associated endonuclease Cas9