SMTL ID : 5b2o.1

Crystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGG PAM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

DT-DG-DG-DT-DA-DT-DC-DG-DG.1: 26 residues within 4Å: Chain A: R.1370, N.1451, K.1454, D.1473, S.1476, R.1477, K.1482, W.1510, P.1512, N.1556, N.1557, S.1558, R.1559, K.1561, R.1588, Y.1589, E.1606 Chain C: C.1, C.2, G.3, A.4, T.5, A.6, C.7, C.8, A.9 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.1244, A:D.1245, A:D.1245, A:D.1245, A:G.1246, A:R.1559, A:R.1588, A:K.1612 Water bridges: A:R.61, A:Y.1248, A:Y.1248, A:R.1477, A:R.1477 Salt bridges: A:K.1388, A:K.1586 pi-Cation interactions: A:R.1477, A:R.1477

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.463, C.660, C.817, C.820 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.463, A:C.660, A:C.817, A:C.820

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: F.650, D.652 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.652, A:D.652 Water bridges: A:F.650, A:D.652 NA.4: 2 residues within 4Å: Chain A: N.1251 Ligands: ACT.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1251 NA.30: 4 residues within 4Å: Chain B: G.28, U.30, U.45 Ligands: NA.31 No protein-ligand interaction detected (PLIP) NA.31: 3 residues within 4Å: Chain B: G.28, U.45 Ligands: NA.30 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: K.567, I.604, F.605, H.612 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: K.369, P.370, K.373, H.397, W.398, E.402 Ligand excluded by PLIP

17 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.7: 3 residues within 4Å: Chain A: D.14, E.906, H.1165 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:H.1165, H2O.1, H2O.3 CA.8: 2 residues within 4Å: Chain A: D.69 Chain B: A.60 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.69, H2O.21, H2O.26, H2O.28, H2O.35 CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain A: D.69 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.69, H2O.11, H2O.27, H2O.29, H2O.34 CA.11: 2 residues within 4Å: Chain A: V.405 Chain B: U.83 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:V.405, H2O.21, H2O.27, H2O.36 CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain A: S.510 Chain B: U.84 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.510, H2O.20, H2O.21, H2O.22, H2O.31 CA.14: 2 residues within 4Å: Chain A: K.1418, D.1420 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.1418, A:D.1420, H2O.11, H2O.22, H2O.22 CA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 5 residues within 4Å: Chain A: E.1234, N.1237, I.1500, D.1501, S.1502 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.1234, A:S.1502 CA.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.33: 1 residues within 4Å: Chain B: U.93 No protein-ligand interaction detected (PLIP) CA.34: 1 residues within 4Å: Chain B: G.74 No protein-ligand interaction detected (PLIP) CA.35: 1 residues within 4Å: Chain A: K.1439 No protein-ligand interaction detected (PLIP) CA.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.37: 2 residues within 4Å: Chain B: G.20, G.21 No protein-ligand interaction detected (PLIP) CA.38: 3 residues within 4Å: Chain B: U.12, G.13 Chain C: C.18 No protein-ligand interaction detected (PLIP)

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

EDO.17: 6 residues within 4Å: Chain A: K.48, Y.51, T.52, L.53, L.54, V.914 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: S.310, G.312 Chain B: G.19, G.20 Chain C: C.13 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: D.93, T.94, Y.335, N.338, F.339, N.342, Y.348 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: H.397, L.400, G.401 Chain B: G.85, C.87 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: L.629, Y.630, I.631, Y.659, I.856, R.1096, E.1100 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: R.628, L.629, Y.630, S.1121, F.1122 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: K.462, G.648, F.650, N.661 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: P.1254, Y.1268, Y.1332 Chain B: C.42 Ligands: EDO.39, EDO.44 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: S.108, I.110, D.409, K.412, P.450, P.451, Y.452 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: L.9, S.24, A.25, F.26, N.38, N.40, N.880, N.883 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: Q.481, Y.533, K.534, D.537 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: S.902, A.904, F.907, N.1092, T.1094 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain A: Y.1268 Chain B: C.42, G.43 Ligands: EDO.24, EDO.44 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain A: E.1404, R.1407, F.1427, F.1428, L.1446 Chain B: G.31, C.44, U.45 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain A: R.62, R.65 Chain B: A.61, G.62 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain A: S.108, Y.452, L.453 Chain B: U.17, G.18 Chain C: G.15 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain A: K.369, R.372 Chain B: G.73, C.89 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain A: T.1327, Y.1332 Chain B: C.34, C.35, G.41, C.42 Ligands: EDO.24, EDO.39 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain A: M.55, R.58, K.867 Chain B: A.64, G.69 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain B: A.71, G.94 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain B: C.32, G.33, C.34 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain A: R.458, K.459 Chain B: A.71, C.72, C.89 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain A: N.1092, G.1093, T.1094 Chain C: C.21, T.22 Ligand excluded by PLIP

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

ACT.29: 6 residues within 4Å: Chain A: Q.95, T.1461, W.1462, D.1463, N.1465 Chain B: A.50 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.95, A:D.1463 Hydrogen bonds: A:T.1461, A:D.1463, A:N.1465 ACT.49: 7 residues within 4Å: Chain A: N.1251, S.1371, R.1373, F.1401, P.1447 Chain B: C.44 Ligands: NA.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.1401, A:P.1447 Hydrogen bonds: A:S.1371, A:S.1371 Water bridges: A:R.1373, A:R.1373, A:R.1373, A:R.1373 Salt bridges: A:R.1373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, H. et al., Structure and Engineering of Francisella novicida Cas9. Cell (2016)

Release Date

2016-03-02

Peptides

CRISPR-associated endonuclease Cas9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CRISPR-associated endonuclease Cas9

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