SMTL ID : 6ai6.1

Crystal structure of SpCas9-NG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x DT- DG- DG- DT- DA- DT- DT- DG: DNA (8-MER)(Non-covalent)

DT-DG-DG-DT-DA-DT-DT-DG.1: 22 residues within 4Å: Chain A: R.1118, S.1120, K.1122, S.1140, P.1141, V.1143, K.1204, A.1219, S.1220, F.1223, Q.1225, A.1324, R.1337, R.1341 Chain C: C.1, A.2, A.3, T.4, A.5, C.6, C.7, A.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.1111, A:E.1112, A:E.1112, A:S.1113, A:R.1115, A:R.1337, A:R.1341, A:S.1342, A:S.1342 Salt bridges: A:K.1111, A:K.1338

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

K.2: 5 residues within 4Å: Chain A: L.627, T.628, F.630, Y.660, T.661 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.628, A:F.630, A:Y.660 K.3: 5 residues within 4Å: Chain A: G.365, Y.366, G.369, G.370, A.371 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.369, A:A.371 K.4: 1 residues within 4Å: Chain A: E.61 No protein-ligand interaction detected (PLIP) K.5: 1 residues within 4Å: Chain A: K.115 No protein-ligand interaction detected (PLIP) K.6: 3 residues within 4Å: Chain A: I.230, L.233, E.236 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.230, A:L.233 K.7: 3 residues within 4Å: Chain A: E.588, R.590, N.592 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.588, A:R.590 K.8: 2 residues within 4Å: Chain A: Q.1354 Chain B: A.68 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.1354, H2O.1 K.9: 3 residues within 4Å: Chain A: D.368, G.369 Chain B: U.22 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.369 K.14: 3 residues within 4Å: Chain A: T.1106 Chain B: A.65, U.66 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1106 K.15: 1 residues within 4Å: Chain B: G.21 No protein-ligand interaction detected (PLIP)

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

MG.10: 1 residues within 4Å: Chain B: G.19 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain B: U.50, A.52 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: G.21, U.22 No protein-ligand interaction detected (PLIP)

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

EDO.11: 4 residues within 4Å: Chain A: R.465 Chain B: G.62, U.63, U.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.465, A:R.465 Water bridges: A:R.70 EDO.12: 6 residues within 4Å: Chain A: F.1109, I.1172, M.1173, R.1175, S.1176 Chain B: A.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1173, A:R.1175, A:S.1176 EDO.13: 8 residues within 4Å: Chain A: Y.140, R.143, H.164, F.168, N.411, H.419 Chain B: G.19, C.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.143, A:N.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimasu, H. et al., Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science (2018)

Release Date

2018-10-31

Peptides

CRISPR-associated endonuclease Cas9/Csn1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CRISPR-associated endonuclease Cas9/Csn1