SMTL ID : 5b2t.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

DT-DG-DC-DG-DA-DT-DT-DG.1: 23 residues within 4Å: Chain B: K.1111, R.1118, S.1120, K.1122, S.1140, K.1204, A.1219, S.1220, R.1222, E.1223, Q.1225, A.1324, R.1337, E.1339, R.1341 Chain C: C.1, A.2, A.3, T.4, C.5, G.6, C.7, A.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.1111, B:E.1112, B:S.1113, B:R.1337, B:R.1341 Water bridges: B:S.1113, B:S.1113, B:D.1288, B:D.1288, B:E.1339 Salt bridges: B:K.1293, B:K.1338

10 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.1, H2O.5, H2O.17 K.3: 3 residues within 4Å: Chain A: A.68 Chain B: Q.1354, S.1355 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:Q.1354, H2O.4, H2O.4, H2O.19 K.4: 1 residues within 4Å: Chain A: G.21 No protein-ligand interaction detected (PLIP) 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.23 K.11: 5 residues within 4Å: Chain B: G.365, Y.366, G.369, G.370, A.371 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.366, B:G.369, B:A.371 K.12: 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.13: 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.13, H2O.18, H2O.21, H2O.21 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.21 K.15: 3 residues within 4Å: Chain B: I.230, L.233, E.236 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.230, B:L.233 K.16: 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.21

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

MG.5: 2 residues within 4Å: Chain A: U.50, G.62 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: G.21 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: G.18, G.19 Chain B: R.75 No protein-ligand interaction detected (PLIP)

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

EDO.8: 5 residues within 4Å: Chain A: G.62, U.63, U.64 Chain B: R.465, F.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.465 Water bridges: B:R.70, B:R.465 EDO.17: 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.18: 6 residues within 4Å: Chain B: S.1281, K.1282, L.1286, A.1287, D.1288, L.1291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.1286, B:A.1287, B:A.1287 EDO.19: 5 residues within 4Å: Chain B: V.1143, G.1169, T.1171, A.1221, R.1222 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.1169, B:G.1169, B:G.1169, 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.143, B:N.411 Water bridges: B:H.419, B:H.419

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

ACT.9: 6 residues within 4Å: Chain A: A.65, U.66, C.67 Chain B: V.1104, 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