SMTL ID : 7oim.1

Mouse RNF213, with mixed nucleotides bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: A.1631, G.1632, V.1633, G.1634, K.1635, S.1636, L.1637, A.1789, M.1790, D.1791, E.1794, W.1848, R.1852, K.2135, S.2210 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.1632, A:V.1633, A:G.1634, A:K.1635, A:S.1636, A:L.1637, A:A.1789, A:D.1791, A:R.1852, A:R.1852, A:S.2210 Salt bridges: A:K.1635, A:K.2135 pi-Stacking: A:W.1848, A:W.1848, A:W.1848

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

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.3637, H.3639, C.3657, C.3660 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.3637, A:H.3639, A:H.3639, A:C.3657, A:C.3660 ZN.4: 4 residues within 4Å: Chain A: C.3622, C.3625, C.3642, C.3645 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.3622, A:C.3625, A:C.3642

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 14 residues within 4Å: Chain A: T.2028, Y.2029, E.2030, N.2035, T.2058, C.2060, G.2061, K.2062, T.2063, Y.2229, Q.2232, I.2233, L.2274, E.2278 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.2029, A:E.2030, A:E.2030, A:K.2062, A:T.2063, A:T.2063, A:T.2063, A:Q.2232, A:E.2278 Salt bridges: A:K.2062 pi-Stacking: A:Y.2229, A:Y.2229 pi-Cation interactions: A:R.2064

1 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.6: 17 residues within 4Å: Chain A: I.2378, A.2379, N.2381, K.2406, P.2407, G.2408, S.2409, S.2410, K.2411, S.2412, L.2413, N.2522, R.2590, Y.2593, K.2597, N.2751, R.2802 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.2379, A:N.2381, A:N.2381, A:K.2406, A:G.2408, A:S.2409, A:S.2410, A:K.2411, A:K.2411, A:S.2412, A:N.2522, A:N.2751 Salt bridges: A:K.2411, A:R.2590, A:R.2590

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahel, J. et al., E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP. To Be Published

Release Date

2022-06-01

Peptides

E3 ubiquitin-protein ligase RNF213: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase RNF213