2NVU
Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | NEDD8-activating enzyme E1 regulatory subunit | polymer | 536 | 60459.2 | 1 | UniProt (Q13564) Pfam (PF00899) | Homo sapiens (human) | Amyloid protein-binding protein 1, Amyloid beta precursor protein-binding protein 1, 59 kDa, APP-BP1, Protooncogene protein 1, HPP1 |
| 2 | B (B) | Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera | polymer | 805 | 89332.8 | 1 | UniProt (Q8TBC4) Pfam (PF01547) UniProt (by SIFTS) (P0AEX9) | Homo sapiens (human) | MBP, Ubiquitin-activating enzyme 3, NEDD8-activating enzyme E1C, Ubiquitin-activating enzyme E1C |
| 3 | C (C) | NEDD8-conjugating enzyme Ubc12 | polymer | 180 | 20665.7 | 1 | UniProt (P61081) Pfam (PF00179) | Homo sapiens (human) | Ubiquitin-conjugating enzyme E2 M, NEDD8 protein ligase, NEDD8 carrier protein |
| 4 | D, E (I, J) | NEDD8 | polymer | 81 | 8919.3 | 2 | UniProt (Q15843) Pfam (PF00240) | Homo sapiens (human) | Ubiquitin-like protein Nedd8, Neddylin |
| 5 | F (B) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 6 | G (B) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 7 | H (B) | ADENOSINE-5'-TRIPHOSPHATE | non-polymer | 507.2 | 1 | Chemie (ATP) | |||
| 8 | I, J, K, L (A, B, C, I) | water | water | 18.0 | 45 | Chemie (HOH) |
Sequence modifications
A: 1 - 534 (UniProt: Q13564)
B: 2012 - 2442 (UniProt: Q8TBC4)
C: 1 - 178 (UniProt: P61081)
I, J: 1 - 76 (UniProt: Q15843)
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | cloning artifact |
| Ser 0 | - | cloning artifact |
| PDB | External Database | Details |
|---|---|---|
| Met 998 | - | SEE REMARK 999 |
| Lys 999 | - | SEE REMARK 999 |
| Leu 1000 | - | SEE REMARK 999 |
| Met 1001 | - | SEE REMARK 999 |
| Ala 1371 | - | SEE REMARK 999 |
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | cloning artifact |
| Ser 0 | - | cloning artifact |
| - | Ser 16 | deletion |
| - | Ala 17 | deletion |
| - | Gly 18 | deletion |
| - | Gly 19 | deletion |
| - | Thr 20 | deletion |
| Ala 111 | Cys 111 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly -4 | - | cloning artifact |
| Ser -3 | - | cloning artifact |
| Gly -2 | - | cloning artifact |
| Gly -1 | - | cloning artifact |
| Ser 0 | - | cloning artifact |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 188296.2 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 596.9 | |
| All* | Total formula weight | 188893.1 |
