MolNFT v1 · #87576 · protein
Crystal structure of the minimal pho-sfmbt complex (P21 spacegroup)
4C5E · Polycomb protein sfmbt: “Crystal structure of the minimal pho-sfmbt complex (P21 spacegroup)”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #87576 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4C5E
- Type
- protein
- Length
- 1,874 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein sfmbt; Polycomb protein pho
- UniProt
- Q9VK33, Q8ST83
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein sfmbt | protein | 440 | 17% helix, 29% strand | Q9VK33 |
| B | Polycomb protein sfmbt | protein | 439 | 18% helix, 29% strand | Q9VK33 |
| C | Polycomb protein sfmbt | protein | 438 | 17% helix, 29% strand | Q9VK33 |
| D | Polycomb protein sfmbt | protein | 437 | 17% helix, 29% strand | Q9VK33 |
| E, F, G, H | Polycomb protein pho | protein | 30 | 0% helix, 67% strand | Q8ST83 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.83 | 0.89 | 55 | empty |
| 2 | 895 | 0.83 | 0.84 | 99 | empty |
| 3 | 1142 | 0.82 | 0.83 | 146 | empty |
| 4 | 600 | 0.82 | 0.87 | 74 | empty |
| 5 | 1174 | 0.79 | 0.81 | 123 | empty |
Interfaces
22 interfaces between chains.
- A–E · 966 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 951 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 943 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 942 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 935 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4C5E · Crystal structure of the minimal Pho-Sfmbt complex (P21 spacegroup) · the same entry in another collection · chain E against E, TM-score 1.00
- Q9VK33 · AlphaFold monomer V2.0 prediction for polycomb protein sfmbt (Q9VK33) · a predicted model of the same protein · chain D 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 Q9VK33
- Every structure of UniProt Q8ST83
- Elsewhere: RCSB PDB 4C5E · PDBe 4C5E · UniProt Q9VK33 · UniProt Q8ST83
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