SMTL ID : 6y5p.1 (1 other biounit)

RING-DTC domain of Deltex1 bound to NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 16 residues within 4Å: Chain A: R.145, G.146, R.149, T.180, S.181, N.182, T.183, T.184, V.190, V.191, W.192, N.193, H.196, H.197, T.199, H.208 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:R.145, A:T.184 Hydrogen bonds: A:S.181, A:N.182, A:T.183, A:T.183, A:V.190, A:W.192, A:W.192, A:H.196, A:H.196, A:T.199 Water bridges: A:R.149, A:R.149, A:R.149, A:N.182, A:H.197, A:H.197, A:T.199, A:H.208 Salt bridges: A:R.149 pi-Stacking: A:W.192, A:H.208, A:H.208

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

EDO.2: 1 residues within 4Å: Chain A: E.31 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.31, A:E.31 EDO.3: 7 residues within 4Å: Chain A: K.17, V.18, K.19, P.21, E.51, L.52, V.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.53, A:V.53 EDO.4: 2 residues within 4Å: Chain A: P.115, D.116 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: I.107, R.121, Y.152, F.201 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: C.29, E.31, G.38, Y.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.29 EDO.7: 8 residues within 4Å: Chain A: D.25, C.26, T.27, L.33, H.61, M.62, Y.63, T.85 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.27, A:M.62 Water bridges: A:M.62, A:M.62

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 7 residues within 4Å: Chain A: C.26, I.28, C.29, S.37, G.38, H.64, C.67 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.26, A:C.29, A:H.64, A:C.67 ZN.9: 5 residues within 4Å: Chain A: C.59, H.61, C.83, T.85, C.86 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.59, A:H.61, A:C.83, A:C.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chatrin, C. et al., Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases. Sci Adv (2020)

Release Date

2020-09-30

Peptides

E3 ubiquitin-protein ligase DTX1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase DTX1

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