SMTL ID : 6fb5.1

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.19 Chain B: G.18 Chain C: C.14 Chain D: A.15 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.19, A:D.19, B:G.18, H2O.1, H2O.5 MG.2: 2 residues within 4Å: Chain A: A.133, N.135 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.133, A:N.135, H2O.1, H2O.1, H2O.2 MG.3: 2 residues within 4Å: Chain B: A.133, N.135 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.133, B:N.135, H2O.2, H2O.3, H2O.3 MG.4: 5 residues within 4Å: Chain A: S.18 Chain B: D.19 Chain C: A.15 Chain D: G.14 Ligands: PGO.6 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:S.18, B:D.19, B:D.19, H2O.2, H2O.4

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

ACT.5: 5 residues within 4Å: Chain A: K.95 Chain B: Y.11, F.53, K.56, E.60 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.11, B:F.53 Water bridges: B:K.56, A:K.95 Salt bridges: B:K.56, A:K.95

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.6: 7 residues within 4Å: Chain A: L.96, K.97, D.136 Chain B: R.50 Chain C: A.15, G.16 Ligands: MG.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.97 Water bridges: B:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prieto, J. et al., Understanding the indirect DNA read-out specificity of I-CreI Meganuclease. Sci Rep (2018)

Release Date

2018-07-18

Peptides

I-CreI monomer A: A
I-CreI monomer B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

I-CreI monomer A

I-CreI monomer B

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