SMTL ID : 3w2w.2 (1 other biounit)

Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.254, C.257, C.284, C.287 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.254, A:C.257, A:C.284, A:C.287 ZN.6: 4 residues within 4Å: Chain C: C.254, C.257, C.284, C.287 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.254, C:C.257, C:C.284, C:C.287

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 17 residues within 4Å: Chain A: K.31, V.33, V.35, Q.36, P.37, I.39, S.52, L.55, S.56, N.106, R.242, D.406, Y.475, D.480 Chain B: R.262 Ligands: ATP.3, MG.5 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.35, A:Q.36, A:Q.36, A:S.52, A:S.56, A:N.106, A:N.106, A:D.406, A:D.480 Water bridges: A:R.537 Salt bridges: A:K.31, A:K.31, A:R.242, B:R.262, B:R.262 pi-Stacking: A:Y.475, A:Y.475 ATP.3: 17 residues within 4Å: Chain A: Y.77, K.107, D.406, G.407, D.408, D.409, M.410, G.411, I.414, H.448, S.452, L.455, K.545, K.550 Chain B: K.111 Ligands: ATP.2, MG.4 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.107, A:G.407, A:D.409, A:M.410, A:G.411, A:S.452 Salt bridges: A:K.545, A:K.550, B:K.111, B:K.111, B:K.111 pi-Stacking: A:Y.77, A:Y.77 ATP.7: 17 residues within 4Å: Chain C: K.31, V.33, V.35, Q.36, P.37, I.39, S.52, L.55, S.56, N.106, R.242, D.406, Y.475, D.480 Chain D: R.262 Ligands: ATP.8, MG.10 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.35, C:Q.36, C:Q.36, C:S.52, C:S.56, C:N.106, C:N.106, C:D.406, C:D.480 Water bridges: C:R.537 Salt bridges: C:K.31, C:K.31, C:R.242, D:R.262, D:R.262 pi-Stacking: C:Y.475, C:Y.475 ATP.8: 17 residues within 4Å: Chain C: Y.77, K.107, D.406, G.407, D.408, D.409, M.410, G.411, I.414, H.448, S.452, L.455, K.545, K.550 Chain D: K.111 Ligands: ATP.7, MG.9 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.107, C:G.407, C:D.409, C:M.410, C:G.411, C:S.452 Salt bridges: C:K.545, C:K.550, D:K.111, D:K.111, D:K.111 pi-Stacking: C:Y.77, C:Y.77

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.406, G.407, K.545 Ligands: ATP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.406, A:G.407, H2O.2 MG.5: 2 residues within 4Å: Chain B: R.262 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: D.406, G.407, K.545 Ligands: ATP.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.406, C:G.407, H2O.5 MG.10: 2 residues within 4Å: Chain D: R.262 Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osawa, T. et al., Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex. J.Mol.Biol. (2013)

Release Date

2013-10-16

Peptides

CRISPR system Cmr subunit Cmr2: AC
CRISPR system Cmr subunit Cmr3: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

CRISPR system Cmr subunit Cmr2

CRISPR system Cmr subunit Cmr3

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