SMTL ID : 6t7f.1

RCR E3 ligase E2-Ubiquitin transthiolation intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.11, C.14, H.34, C.37 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:C.14, A:H.34, A:C.37 ZN.2: 4 residues within 4Å: Chain A: C.29, H.31, C.58, C.61 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.29, A:H.31, A:C.58, A:C.61 ZN.3: 4 residues within 4Å: Chain A: C.127, C.130, C.158, C.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.127, A:C.130, A:C.158, A:C.161 ZN.4: 4 residues within 4Å: Chain A: C.170, H.173, C.252, C.255 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.170, A:H.173, A:C.252, A:C.255 ZN.5: 4 residues within 4Å: Chain A: C.182, C.185, C.200, C.203 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.182, A:C.185, A:C.200, A:C.203 ZN.6: 4 residues within 4Å: Chain A: C.186, C.221, C.235, H.241 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.186, A:C.221, A:C.235, A:H.241

1 x LWZ: 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide(Covalent)

LWZ.7: 8 residues within 4Å: Chain A: C.141, D.142 Chain B: N.80, C.88, L.89, N.117, D.120 Chain C: R.72 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.72, B:N.80, B:N.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabbitt, P.D. et al., Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity. Nat.Chem.Biol. (2020)

Release Date

2020-08-05

Peptides

E3 ubiquitin-protein ligase MYCBP2: A
Ubiquitin-conjugating enzyme E2 D3: B
Polyubiquitin-C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase MYCBP2

Ubiquitin-conjugating enzyme E2 D3

Polyubiquitin-C

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