MolNFT v1 · #148501 · protein
Co-crystal structure of spop math domain and hamster PDX1 fragment
6F8G · Speckle-type poz protein: “Co-crystal structure of spop math domain and hamster PDX1 fragment”. X-ray diffraction, 6 pockets (best druggability 0.80). MolNFT v1 #148501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F8G
- Type
- protein
- Length
- 607 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Speckle-type poz protein; PANCREAS/DUODENUM homeobox protein 1
- UniProt
- O43791, P70118
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Speckle-type poz protein | protein | 142 | 8% helix, 52% strand | O43791 |
| D | Speckle-type poz protein | protein | 140 | 15% helix, 49% strand | O43791 |
| E, G | PANCREAS/DUODENUM homeobox protein 1 | protein | 11 | 0% helix, 18% strand | P70118 |
| F | PANCREAS/DUODENUM homeobox protein 1 | protein | 10 | 0% helix, 20% strand | P70118 |
| H | PANCREAS/DUODENUM homeobox protein 1 | protein | 9 | 0% helix, 11% strand | P70118 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.80 | 0.82 | 107 | empty |
| 2 | 84 | 0.38 | 0.77 | 18 | empty |
| 3 | 65 | 0.32 | 0.76 | 15 | empty |
| 4 | 56 | 0.30 | 0.75 | 17 | empty |
| 5 | 57 | 0.30 | 0.75 | 15 | empty |
Interfaces
14 interfaces between chains.
- A–B · 976 Ų buried · 18 hydrogen bonds · protein-protein
- D–G · 763 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 657 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 648 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 607 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6F8G · Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment · the same entry in another collection · chain H against H, TM-score 1.00
- O43791 · AlphaFold monomer V2.0 prediction for speckle-type poz protein (O43791) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P70118 · AlphaFold monomer V2.0 prediction for PANCREAS/DUODENUM homeobox protein 1 (P70118) · a predicted model of the same protein · chain E against A, TM-score 0.48
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 O43791
- Every structure of UniProt P70118
- Elsewhere: RCSB PDB 6F8G · PDBe 6F8G · UniProt O43791 · UniProt P70118
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