MolNFT v1 · #180739 · protein
Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex
7L9P · Pachytene checkpoint protein 2 homolog: “Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex”. Electron microscopy, 1 ligand (AGS), 20 pockets (best druggability 0.85). MolNFT v1 #180739 on GenesisL1: 3D structure, binding…
- PDB
- 7L9P
- Type
- protein
- Length
- 2,919 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pachytene checkpoint protein 2 homolog; Mitotic spindle assembly checkpoint protein…
- UniProt
- Q15645, Q9UI95, Q86V20, Q6ZNX1
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pachytene checkpoint protein 2 homolog | protein | 308 | 49% helix, 11% strand | Q15645 |
| B, C, D, E | Pachytene checkpoint protein 2 homolog | protein | 398 | 43% helix, 13% strand | Q15645 |
| F | Pachytene checkpoint protein 2 homolog | protein | 272 | 43% helix, 13% strand | Q15645 |
| G | Mitotic spindle assembly checkpoint protein MAD2B | protein | 172 | 35% helix, 28% strand | Q9UI95 |
| I | Mitotic spindle assembly checkpoint protein MAD2B | protein | 189 | 26% helix, 24% strand | Q9UI95 |
| J | Mitotic spindle assembly checkpoint protein MAD2B | protein | 127 | 43% helix, 17% strand | Q9UI95 |
| K | Mitotic spindle assembly checkpoint protein MAD2B | protein | 127 | 41% helix, 16% strand | Q9UI95 |
| Y | Shieldin complex subunit 2, shieldin complex subunit 3 chimera | protein | 69 | 12% helix, 9% strand | Q86V20, Q6ZNX1 |
| X | Shieldin complex subunit 2, shieldin complex subunit 3 chimera | protein | 63 | 17% helix, 13% strand | Q6ZNX1 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E, F
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 | 959 | 0.85 | 0.86 | 137 | empty |
| 2 | 1103 | 0.83 | 0.84 | 110 | AGS |
| 3 | 817 | 0.83 | 0.86 | 72 | AGS |
| 4 | 992 | 0.82 | 0.83 | 76 | AGS |
| 5 | 654 | 0.81 | 0.86 | 66 | AGS |
Interfaces
24 interfaces between chains.
- D–E · 2437 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2300 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2231 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1928 Ų buried · 9 hydrogen bonds · protein-protein
- I–Y · 1263 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7L9P · Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex · the same entry in another collection · chain A against A, 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 Q15645
- Every structure of UniProt Q9UI95
- Every structure of UniProt Q86V20
- Every structure of UniProt Q6ZNX1
- Elsewhere: RCSB PDB 7L9P · PDBe 7L9P · UniProt Q15645 · UniProt Q9UI95 · UniProt Q86V20 · UniProt Q6ZNX1
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