Research workbench
S. cerevisiae APC/C-CDH1 complex
Analyse S. cerevisiae APC/C-CDH1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A3T
- Type
- protein
- Length
- 7,661 residues
- Chains
- 19
- 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, P53068, A0A6A5PYD7, A0A8H4BYV4, P53886, Q08683, P16522, Q12379, P40577, Q04601, Q12440, Q12157
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 19 distinct chains · 57% helix, 9% 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 | 72% helix, 0% strand | P09798 |
| K | Anaphase-promoting complex subunit CDC16 | protein | 505 | 74% helix, 0% strand | P09798 |
| G | Anaphase-promoting complex subunit CDC26 | protein | 35 | 63% helix, 0% strand | P14724 |
| W | Anaphase-promoting complex subunit CDC26 | protein | 37 | 65% helix, 0% strand | P14724 |
| H | Anaphase-promoting complex subunit CDC27 | protein | 505 | 76% helix, 0% strand | P38042 |
| E | Anaphase-promoting complex subunit 9 | protein | 130 | 59% helix, 2% strand | Q12107 |
| A | Anaphase-promoting complex subunit DOC1 | protein | 219 | 15% helix, 31% strand | P53068 |
| B | CDH1 isoform 1 | protein | 440 | 15% helix, 34% strand | A0A6A5PYD7 |
| S | HSL1 isoform 1 | protein | 6 | 0% helix, 0% strand | A0A8H4BYV4 |
| C | Anaphase-promoting complex subunit 1 | protein | 1410 | 44% helix, 13% strand | P53886 |
| O | Anaphase-promoting complex subunit 5 | protein | 658 | 67% helix, 2% strand | Q08683 |
| D | Anaphase-promoting complex subunit CDC23 | protein | 560 | 70% helix, 0% strand | P16522 |
| P | Anaphase-promoting complex subunit CDC23 | protein | 556 | 70% helix, 0% strand | P16522 |
| I | Anaphase-promoting complex subunit SWM1 | protein | 111 | 41% 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, 24% strand | Q04601 |
| T | Anaphase-promoting complex subunit 2 | protein | 645 | 66% helix, 6% strand | Q12440 |
| U | Anaphase-promoting complex subunit 11 (EC 6.3.2.-) | protein | 114 | 25% helix, 24% strand | Q12157 |
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 | 1163 | 0.87 | 0.88 | 134 | empty |
| 2 | 903 | 0.86 | 0.88 | 86 | empty |
| 3 | 988 | 0.85 | 0.86 | 104 | empty |
| 4 | 1072 | 0.83 | 0.84 | 118 | empty |
| 5 | 953 | 0.83 | 0.84 | 83 | empty |
Interfaces
48 interfaces between chains.
- O–Q · 3388 Ų buried · 36 hydrogen bonds · protein-protein
- C–O · 3168 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 3047 Ų buried · 45 hydrogen bonds · protein-protein
- F–H · 2658 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2628 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 8A3T · S. cerevisiae APC/C-Cdh1 complex · the same entry in another collection · chain C against C, 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 P53068
- Every structure of UniProt A0A6A5PYD7
- Every structure of UniProt A0A8H4BYV4
- 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 Q12440
- Every structure of UniProt Q12157
- Elsewhere: RCSB PDB 8A3T · PDBe 8A3T · UniProt P38042 · UniProt P09798 · UniProt P14724 · UniProt Q12107 · UniProt P53068 · UniProt A0A6A5PYD7 · UniProt A0A8H4BYV4 · UniProt P53886 · UniProt Q08683 · UniProt P16522 · UniProt Q12379 · UniProt P40577 · UniProt Q04601 · UniProt Q12440 · UniProt Q12157
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