RCR E3 ligase E2-Ubiquitin transthiolation intermediate. Determined by X-ray diffraction at 2.58 Å resolution. Released 5 Aug 2020.
Explore 6T7F in 3D Show helices and sheets RCSB PDB PDBe
6T7F contains 29 α-helices and 31 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4389 | 1 | 1 |
| β-strand | 4397 | 1 | 1 |
| α-helix | 4398-4400 | 3 | |
| β-strand | 4403-4405 | 3 | 2 |
| β-strand | 4411-4413 | 3 | 2 |
| α-helix | 4414-4423 | 10 | |
| β-strand | 4429-4430 | 2 | 3 |
| α-helix | 4433-4435 | 3 | |
| β-strand | 4436 | 1 | 4 |
| β-strand | 4443 | 1 | 4 |
| α-helix | 4444 | 1 | |
| α-helix | 4447-4449 | 3 | |
| α-helix | 4450-4473 | 24 | |
| α-helix | 4480-4483 | 4 | |
| α-helix | 4493-4500 | 8 | |
| β-strand | 4501-4505 | 5 | 3 |
| β-strand | 4512-4517 | 6 | 3 |
| α-helix | 4518-4519 | 2 | |
| α-helix | 4532-4534 | 3 | |
| β-strand | 4535 | 1 | 5 |
| α-helix | 4538-4541 | 4 | |
| α-helix | 4546-4549 | 4 | |
| β-strand | 4557-4559 | 3 | 6 |
| β-strand | 4560 | 1 | 7 |
| β-strand | 4567 | 1 | 7 |
| β-strand | 4570-4572 | 3 | 5 |
| β-strand | 4576-4578 | 3 | 5 |
| α-helix | 4580-4584 | 5 | |
| α-helix | 4586-4591 | 6 | |
| α-helix | 4594-4596 | 3 | |
| α-helix | 4598-4599 | 2 | |
| β-strand | 4602 | 1 | 8 |
| α-helix | 4604-4606 | 3 | |
| β-strand | 4608 | 1 | 8 |
| β-strand | 4628-4631 | 4 | 6 |
| α-helix | 4632-4635 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | -1-13 | 15 | |
| α-helix | 17-18 | 2 | |
| β-strand | 21-25 | 5 | 9 |
| β-strand | 32-38 | 7 | 9 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 9 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 9 |
| β-strand | 75 | 1 | 10 |
| β-strand | 78 | 1 | 10 |
| β-strand | 83 | 1 | 9 |
| β-strand | 84 | 1 | 10 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 12-15 | 4 | 11 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 11 |
| β-strand | 48-49 | 2 | 11 |
| α-helix | 50-51 | 2 | |
| β-strand | 66-71 | 6 | 11 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| E3 ubiquitin-protein ligase MYCBP2 | A | protein | 261 | Homo sapiens | O75592 |
| Ubiquitin-conjugating enzyme E2 D3 | B | protein | 150 | Homo sapiens | P61077 (AlphaFold model) |
| Polyubiquitin-C | C | protein | 73 | Homo sapiens | P0CG48 (AlphaFold model) |
>6T7F_1 E3 ubiquitin-protein ligase MYCBP2 (chains A) GPLGSDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI CKNKINHIVLKDLLDPIKELYEDVRRKALMRLEYEGLHKSEAITTPGVRFYNDPAGYAMN RYAYYVCYKCRKAYFGGEARCDAEAGRGDDYDPRELICGACSDVSRAQMCPKHGTDFLEY KCRYCCSVAVFFCFGTTHFCNACHDDFQRMTSIPKEELPHCPAGPKGKQLEGTECPLHVV HPPTGEEFALGCGVCRNAHTF
>6T7F_2 Ubiquitin-conjugating enzyme E2 D3 (chains B) GPGSALKRINKELSDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFP TDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDD PLVPEIARIYKTDRDKYNRISREWTQKYAM
>6T7F_3 Polyubiquitin-C (chains C) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRL
| ID | Name | Formula | Copies |
|---|---|---|---|
| LWZ | 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide | C6 H10 N4 O S2 | 1 |
| ZN | Zinc ion | Zn | 6 |
Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity. Mabbitt, P.D., Loreto, A., Dery, M.A. et al. Nat Chem Biol (2020) 16:1227-1236. DOI 10.1038/s41589-020-0598-6 · PubMed
Other PDB entries of the same protein (UniProt O75592), best resolution first:
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