Research workbench
Structure of the human apc-CDH1-HSL1-UBCH10 complex.
Analyse Structure of the human apc-CDH1-HSL1-UBCH10 complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A31
- Type
- protein
- Length
- 8,624 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit 1; Anaphase-promoting complex subunit 11; Cell…
- EC
- 2.3.2.23, 2.3.2.24
- UniProt
- Q9NYG5, Q9UJX2, P60006, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q2NKV2, Q9UJX4, Q9UJX3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 23 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaphase-promoting complex subunit 1 | protein | 1441 | 43% helix, 14% strand | — |
| B | Anaphase-promoting complex subunit 11 | protein | 84 | 13% helix, 26% strand | Q9NYG5 |
| C | Cell division cycle protein 23 homolog | protein | 524 | 76% helix, 0% strand | Q9UJX2 |
| D | Anaphase-promoting complex subunit 15 | protein | 55 | 36% helix, 0% strand | P60006 |
| E | Anaphase-promoting complex subunit 16 | protein | 56 | 77% helix, 0% strand | Q96DE5 |
| F | Anaphase-promoting complex subunit 3 | protein | 498 | 77% helix, 0% strand | P30260 |
| G, W | Anaphase-promoting complex subunit CDC26 | protein | 25 | 48% helix, 0% strand | Q8NHZ8 |
| H | Anaphase-promoting complex subunit 3 | protein | 483 | 78% helix, 0% strand | P30260 |
| I | Anaphase-promoting complex subunit 4 | protein | 730 | 33% helix, 25% strand | Q9UJX5 |
| J | Anaphase-promoting complex subunit 6 | protein | 504 | 75% helix, 0% strand | Q13042 |
| K | Anaphase-promoting complex subunit 6 | protein | 493 | 79% helix, 0% strand | Q13042 |
| L | Anaphase-promoting complex subunit 10 | protein | 182 | 12% helix, 36% strand | Q9UM13 |
| M | Anaphase-promoting complex subunit 13 | protein | 59 | 22% helix, 0% strand | Q2NKV2 |
| N | Anaphase-promoting complex subunit 2 | protein | 703 | 61% helix, 3% strand | — |
| O | Anaphase-promoting complex subunit 5 | protein | 685 | 77% helix, 0% strand | Q9UJX4 |
| P | Cell division cycle protein 23 homolog | protein | 491 | 77% helix, 0% strand | Q9UJX2 |
| Q | Fusion protein - ubiquitin-conjugating enzyme E2 C, ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23, 2.3.2.24) | protein | 162 | 39% helix, 17% strand | — |
| R | The anaphase-promoting complex chain R | protein | 386 | 6% helix, 39% strand | — |
| T | The anaphase-promoting complex chain T | protein | 21 | 0% helix, 0% strand | — |
| U | The anaphase-promoting complex chain U | protein | 24 | 63% helix, 0% strand | — |
| V | The anaphase-promoting complex chain V | protein | 13 | 0% helix, 0% strand | — |
| X | Anaphase-promoting complex subunit 7 | protein | 484 | 80% helix, 0% strand | Q9UJX3 |
| Y | Anaphase-promoting complex subunit 7 | protein | 496 | 80% helix, 0% strand | Q9UJX3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B
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 | 998 | 0.88 | 0.90 | 127 | empty |
| 2 | 1183 | 0.86 | 0.87 | 86 | empty |
| 3 | 981 | 0.86 | 0.87 | 98 | empty |
| 4 | 1140 | 0.85 | 0.85 | 123 | empty |
| 5 | 534 | 0.84 | 0.90 | 57 | empty |
Interfaces
62 interfaces between chains.
- A–O · 4498 Ų buried · 38 hydrogen bonds · protein-protein
- I–O · 3243 Ų buried · 22 hydrogen bonds · protein-protein
- F–H · 3053 Ų buried · 25 hydrogen bonds · protein-protein
- J–K · 2802 Ų buried · 28 hydrogen bonds · protein-protein
- X–Y · 2660 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 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 H against A, TM-score 0.97
- 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 0.96
- 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
- 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 0.95
- Q9UJX2 · AlphaFold monomer V2.0 prediction for cell division cycle protein 23 homolog (Q9UJX2) · a predicted model of the same protein · chain C against A, TM-score 0.94
- 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 0.90
- Q9NYG5 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 11 (Q9NYG5) · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q9NYG5
- Every structure of UniProt Q9UJX2
- Every structure of UniProt P60006
- Every structure of UniProt Q96DE5
- Every structure of UniProt P30260
- Every structure of UniProt Q8NHZ8
- Every structure of UniProt Q9UJX5
- Every structure of UniProt Q13042
- Every structure of UniProt Q9UM13
- Every structure of UniProt Q2NKV2
- Every structure of UniProt Q9UJX4
- Every structure of UniProt Q9UJX3
- Elsewhere: RCSB PDB 5A31 · PDBe 5A31 · UniProt Q9NYG5 · UniProt Q9UJX2 · UniProt P60006 · UniProt Q96DE5 · UniProt P30260 · UniProt Q8NHZ8 · UniProt Q9UJX5 · UniProt Q13042 · UniProt Q9UM13 · UniProt Q2NKV2 · UniProt Q9UJX4 · UniProt Q9UJX3
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