Research workbench
S. cerevisiae apo unphosphorylated APC/C
Analyse S. cerevisiae apo unphosphorylated APC/C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A5Y
- Type
- protein
- Length
- 7,213 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit CDC27; Anaphase-promoting complex subunit CDC16…
- EC
- 6.3.2.-
- UniProt
- P38042, P09798, P14724, Q12107, Q12440, Q12157, P53886, Q08683, P16522, Q12379, P40577, Q04601, P53068
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 16 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Anaphase-promoting complex subunit CDC27 | protein | 502 | 77% helix, 0% strand | P38042 |
| J | Anaphase-promoting complex subunit CDC16 | protein | 509 | 73% helix, 0% strand | P09798 |
| K | Anaphase-promoting complex subunit CDC16 | protein | 505 | 75% helix, 0% strand | P09798 |
| G, W | Anaphase-promoting complex subunit CDC26 | protein | 35 | 60% helix, 0% strand | P14724 |
| H | Anaphase-promoting complex subunit CDC27 | protein | 505 | 75% helix, 0% strand | P38042 |
| E | Anaphase-promoting complex subunit 9 | protein | 130 | 58% helix, 0% strand | Q12107 |
| T | Anaphase-promoting complex subunit 2 | protein | 650 | 64% helix, 6% strand | Q12440 |
| U | Anaphase-promoting complex subunit 11 (EC 6.3.2.-) | protein | 114 | 23% helix, 25% strand | Q12157 |
| C | Anaphase-promoting complex subunit 1 | protein | 1406 | 45% helix, 13% strand | P53886 |
| O | Anaphase-promoting complex subunit 5 | protein | 658 | 66% helix, 2% strand | Q08683 |
| D | Anaphase-promoting complex subunit CDC23 | protein | 560 | 71% helix, 0% strand | P16522 |
| P | Anaphase-promoting complex subunit CDC23 | protein | 556 | 71% helix, 0% strand | P16522 |
| I | Anaphase-promoting complex subunit SWM1 | protein | 111 | 39% helix, 8% strand | Q12379 |
| N | Anaphase-promoting complex subunit MND2 | protein | 96 | 47% helix, 4% strand | P40577 |
| Q | Anaphase-promoting complex subunit 4 | protein | 623 | 39% helix, 25% strand | Q04601 |
| A | Anaphase-promoting complex subunit DOC1 | protein | 218 | 16% helix, 32% strand | P53068 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.87 | 0.88 | 106 | empty |
| 2 | 988 | 0.86 | 0.87 | 102 | empty |
| 3 | 819 | 0.86 | 0.88 | 91 | empty |
| 4 | 1055 | 0.84 | 0.85 | 89 | empty |
| 5 | 1157 | 0.82 | 0.83 | 91 | empty |
Interfaces
37 interfaces between chains.
- O–Q · 3275 Ų buried · 30 hydrogen bonds · protein-protein
- J–K · 3074 Ų buried · 43 hydrogen bonds · protein-protein
- C–O · 2614 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 2605 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2465 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 8A5Y · S. cerevisiae apo unphosphorylated APC/C. · the same entry in another collection · chain O against O, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P38042
- Every structure of UniProt P09798
- Every structure of UniProt P14724
- Every structure of UniProt Q12107
- Every structure of UniProt Q12440
- Every structure of UniProt Q12157
- Every structure of UniProt P53886
- Every structure of UniProt Q08683
- Every structure of UniProt P16522
- Every structure of UniProt Q12379
- Every structure of UniProt P40577
- Every structure of UniProt Q04601
- Every structure of UniProt P53068
- Elsewhere: RCSB PDB 8A5Y · PDBe 8A5Y · UniProt P38042 · UniProt P09798 · UniProt P14724 · UniProt Q12107 · UniProt Q12440 · UniProt Q12157 · UniProt P53886 · UniProt Q08683 · UniProt P16522 · UniProt Q12379 · UniProt P40577 · UniProt Q04601 · UniProt P53068
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