3DBR
Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, C, E, G | NEDD8-activating enzyme E1 regulatory subunit | polymer | 531 | 59973.8 | 4 | UniProt (Q13564) Pfam (PF00899) In PDB | Homo sapiens (human) | Amyloid protein-binding protein 1, Amyloid beta protein-binding protein 1, 59 kDa, APP-BP1, Proto-oncogene protein 1 |
| 2 | B, D, F, H | NEDD8-activating enzyme E1 catalytic subunit | polymer | 434 | 48738.7 | 4 | UniProt (Q8TBC4) Pfam (PF00899) Pfam (PF08825) In PDB | Homo sapiens (human) | Ubiquitin- like modifier-activating enzyme 3, Ubiquitin-activating enzyme 3, NEDD8-activating enzyme E1C, Ubiquitin-activating enzyme E1C |
| 3 | I, J, K, L | NEDD8 | polymer | 88 | 9721.2 | 4 | UniProt (Q15843) Pfam (PF00240) In PDB | Homo sapiens (human) | Ubiquitin-like protein Nedd8, Neddylin |
| 4 | B, D, F, H | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) |
Sequence modifications
A, C, E, G: 1 - 534 (UniProt: Q13564)
B, D, F, H: 12 - 442 (UniProt: Q8TBC4)
I, J, K, L: 101 - 176 (UniProt: Q15843)
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
| - | Asn 254 | deletion |
| - | Glu 255 | deletion |
| - | Asn 256 | deletion |
| - | Gly 257 | deletion |
| - | Ala 258 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Met 9 | - | expression tag |
| Lys 10 | - | expression tag |
| Leu 11 | - | expression tag |
| Gln 190 | Arg 211 | engineered mutation |
| Ala 216 | Cys 237 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly 89 | - | expression tag |
| Ser 90 | - | expression tag |
| Arg 91 | - | expression tag |
| Arg 92 | - | expression tag |
| Ala 93 | - | expression tag |
| Ser 94 | - | expression tag |
| Val 95 | - | expression tag |
| Gly 96 | - | expression tag |
| Ser 97 | - | expression tag |
| Gly 98 | - | expression tag |
| Gly 99 | - | expression tag |
| Ser 100 | - | expression tag |
| Arg 172 | Ala 72 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 473734.7 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 261.6 | |
| All* | Total formula weight | 473996.3 |
