Research workbench
High-resolution structure of the anaphase-promoting COMPLEX/CYCLOSOME (APC/C) bound to co-activator CDH1
Analyse High-resolution structure of the anaphase-promoting COMPLEX/CYCLOSOME (APC/C)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QE7
- Type
- protein
- Length
- 8,928 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit 10; Anaphase-promoting complex subunit 15…
- UniProt
- Q9UM13, P60006, Q9H1A4, Q9UJX6, Q9UJX5, Q9UJX4, Q9UKT4, Q13042, Q8NHZ8, Q9BS18, Q96DE5, P30260, Q9UJX3, Q9UJX2, Q9UM11, Q9NYG5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 21 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anaphase-promoting complex subunit 10 | protein | 183 | 10% helix, 44% strand | Q9UM13 |
| D | Anaphase-promoting complex subunit 15 | protein | 56 | 36% helix, 0% strand | P60006 |
| A | Anaphase-promoting complex subunit 1 | protein | 1648 | 41% helix, 15% strand | Q9H1A4 |
| N | Anaphase-promoting complex subunit 2 | protein | 682 | 63% helix, 5% strand | Q9UJX6 |
| I | Anaphase-promoting complex subunit 4 | protein | 742 | 32% helix, 27% strand | Q9UJX5 |
| O | Anaphase-promoting complex subunit 5 | protein | 707 | 72% helix, 0% strand | Q9UJX4 |
| S | F-box only protein 5 | protein | 100 | 18% helix, 17% strand | Q9UKT4 |
| K | Cell division cycle protein 16 homolog | protein | 531 | 70% helix, 0% strand | Q13042 |
| G | Anaphase-promoting complex subunit CDC26 | protein | 27 | 52% helix, 0% strand | Q8NHZ8 |
| W | Anaphase-promoting complex subunit CDC26 | protein | 26 | 46% helix, 0% strand | Q8NHZ8 |
| M | Anaphase-promoting complex subunit 13 | protein | 68 | 15% helix, 3% strand | Q9BS18 |
| H | Anaphase-promoting complex subunit 16 | protein | 58 | 64% helix, 0% strand | Q96DE5 |
| J | Cell division cycle protein 27 homolog | protein | 510 | 75% helix, 0% strand | P30260 |
| P | Cell division cycle protein 27 homolog | protein | 496 | 74% helix, 0% strand | P30260 |
| Q | Cell division cycle protein 16 homolog | protein | 506 | 70% helix, 0% strand | Q13042 |
| Y | Anaphase-promoting complex subunit 7 | protein | 502 | 75% helix, 0% strand | Q9UJX3 |
| U | Cell division cycle protein 23 homolog | protein | 540 | 70% helix, 0% strand | Q9UJX2 |
| V | Cell division cycle protein 23 homolog | protein | 534 | 70% helix, 0% strand | Q9UJX2 |
| Z | Anaphase-promoting complex subunit 7 | protein | 488 | 72% helix, 0% strand | Q9UJX3 |
| R | Fizzy-related protein homolog | protein | 440 | 10% helix, 35% strand | Q9UM11 |
| C | Anaphase-promoting complex subunit 11 | protein | 84 | 12% helix, 32% strand | Q9NYG5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains N, S, C
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 | 1062 | 0.89 | 0.90 | 106 | empty |
| 2 | 927 | 0.86 | 0.88 | 77 | empty |
| 3 | 721 | 0.86 | 0.90 | 109 | empty |
| 4 | 1141 | 0.83 | 0.84 | 102 | empty |
| 5 | 975 | 0.83 | 0.84 | 127 | empty |
Interfaces
63 interfaces between chains.
- A–O · 5750 Ų buried · 55 hydrogen bonds · protein-protein
- I–O · 3405 Ų buried · 45 hydrogen bonds · protein-protein
- J–P · 3172 Ų buried · 28 hydrogen bonds · protein-protein
- A–N · 2907 Ų buried · 36 hydrogen bonds · protein-protein
- K–Q · 2860 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q9H1A4 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 1 (Q9H1A4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9UM13 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 10 (Q9UM13) · a predicted model of the same protein · chain L against A, TM-score 0.98
- P30260 · AlphaFold monomer V2.0 prediction for cell division cycle protein 27 homolog (P30260) · a predicted model of the same protein · chain P against A, TM-score 0.97
- Q9UJX3 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 7 (Q9UJX3) · a predicted model of the same protein · chain Y against A, TM-score 0.95
- Q9UJX2 · AlphaFold monomer V2.0 prediction for cell division cycle protein 23 homolog (Q9UJX2) · a predicted model of the same protein · chain V against A, TM-score 0.93
- Q9UM11 · AlphaFold monomer V2.0 prediction for fizzy-related protein homolog (Q9UM11) · a predicted model of the same protein · chain R against A, TM-score 0.93
- Q9UJX4 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 5 (Q9UJX4) · a predicted model of the same protein · chain O against A, TM-score 0.93
- Q13042 · AlphaFold monomer V2.0 prediction for cell division cycle protein 16 homolog (Q13042) · a predicted model of the same protein · chain K against A, TM-score 0.92
- Q9UJX5 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 4 (Q9UJX5) · a predicted model of the same protein · chain I against A, TM-score 0.89
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 Q9UM13
- Every structure of UniProt P60006
- Every structure of UniProt Q9H1A4
- Every structure of UniProt Q9UJX6
- Every structure of UniProt Q9UJX5
- Every structure of UniProt Q9UJX4
- Every structure of UniProt Q9UKT4
- Every structure of UniProt Q13042
- Every structure of UniProt Q8NHZ8
- Every structure of UniProt Q9BS18
- Every structure of UniProt Q96DE5
- Every structure of UniProt P30260
- Every structure of UniProt Q9UJX3
- Every structure of UniProt Q9UJX2
- Every structure of UniProt Q9UM11
- Every structure of UniProt Q9NYG5
- Elsewhere: RCSB PDB 7QE7 · PDBe 7QE7 · UniProt Q9UM13 · UniProt P60006 · UniProt Q9H1A4 · UniProt Q9UJX6 · UniProt Q9UJX5 · UniProt Q9UJX4 · UniProt Q9UKT4 · UniProt Q13042 · UniProt Q8NHZ8 · UniProt Q9BS18 · UniProt Q96DE5 · UniProt P30260 · UniProt Q9UJX3 · UniProt Q9UJX2 · UniProt Q9UM11 · UniProt Q9NYG5
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