MolNFT v1 · #119572 · protein
Structure of the human apc-CDC20-HSL1 complex
5G04 · Anaphase-promoting complex subunit 1: “Structure of the human apc-CDC20-HSL1 complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #119572 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5G04
- Type
- protein
- Length
- 8,322 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase-promoting complex subunit 1; Anaphase-promoting complex subunit 11; Cell…
- EC
- 2.7.11.1
- UniProt
- Q9H1A4, Q9NYG5, Q9UJX2, P60006, Q96DE5, P30260, Q8NHZ8, Q9UJX5, Q13042, Q9UM13, Q9BS18, Q9UJX6, Q9UJX4, Q12834, P34244, Q9UJX3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 20 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaphase-promoting complex subunit 1 | protein | 1437 | 40% helix, 12% strand | Q9H1A4 |
| B | Anaphase-promoting complex subunit 11 | protein | 84 | 13% helix, 25% strand | Q9NYG5 |
| C | Cell division cycle protein 23 homolog | protein | 524 | 73% 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 | 84% helix, 0% strand | Q96DE5 |
| F | Cell division cycle protein 27 homolog | protein | 498 | 77% helix, 0% strand | P30260 |
| G, W | Anaphase-promoting complex subunit CDC26 | protein | 25 | 48% helix, 0% strand | Q8NHZ8 |
| H | Cell division cycle protein 27 homolog | protein | 483 | 78% helix, 0% strand | P30260 |
| I | Anaphase-promoting complex subunit 4 | protein | 730 | 33% helix, 25% strand | Q9UJX5 |
| J | Cell division cycle protein 16 homolog | protein | 504 | 75% helix, 0% strand | Q13042 |
| K | Cell division cycle protein 16 homolog | protein | 493 | 79% helix, 0% strand | Q13042 |
| L | Anaphase-promoting complex subunit 10 | protein | 182 | 9% helix, 37% strand | Q9UM13 |
| M | Anaphase-promoting complex subunit 13 | protein | 59 | 20% helix, 0% strand | Q9BS18 |
| N | Anaphase-promoting complex subunit 2 | protein | 631 | 59% helix, 2% strand | Q9UJX6 |
| O | Anaphase-promoting complex subunit 5 | protein | 685 | 75% helix, 0% strand | Q9UJX4 |
| P | Cell division cycle protein 23 homolog | protein | 491 | 76% helix, 0% strand | Q9UJX2 |
| R | Cell division cycle protein 20 homolog | protein | 370 | 8% helix, 42% strand | Q12834 |
| S | Probable SERINE/THREONINE-protein kinase HSL1 (EC 2.7.11.1) | protein | 10 | 0% helix, 0% strand | P34244 |
| X | Anaphase-promoting complex subunit 7 | protein | 484 | 79% 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 | 840 | 0.86 | 0.88 | 82 | empty |
| 2 | 1174 | 0.86 | 0.87 | 87 | empty |
| 3 | 525 | 0.84 | 0.91 | 63 | empty |
| 4 | 1149 | 0.83 | 0.84 | 95 | empty |
| 5 | 1057 | 0.83 | 0.84 | 88 | empty |
Interfaces
52 interfaces between chains.
- A–O · 4655 Ų buried · 51 hydrogen bonds · protein-protein
- I–O · 3309 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 3121 Ų buried · 24 hydrogen bonds · protein-protein
- X–Y · 2900 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 2900 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5G04 · Structure of the human APC-Cdc20-Hsl1 complex · the same entry in another collection · chain G against G, 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 Q9H1A4
- 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 Q9BS18
- Every structure of UniProt Q9UJX6
- Every structure of UniProt Q9UJX4
- Every structure of UniProt Q12834
- Every structure of UniProt P34244
- Every structure of UniProt Q9UJX3
- Elsewhere: RCSB PDB 5G04 · PDBe 5G04 · UniProt Q9H1A4 · UniProt Q9NYG5 · UniProt Q9UJX2 · UniProt P60006 · UniProt Q96DE5 · UniProt P30260 · UniProt Q8NHZ8 · UniProt Q9UJX5 · UniProt Q13042 · UniProt Q9UM13 · UniProt Q9BS18 · UniProt Q9UJX6 · UniProt Q9UJX4 · UniProt Q12834 · UniProt P34244 · UniProt Q9UJX3
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