MolNFT v1 · #154787 · protein
Crystal structure of STH1 bromodomain
6KMB · Nuclear protein STH1/NPS1: “Crystal structure of STH1 bromodomain”. X-ray diffraction, 5 pockets (best druggability 0.84). MolNFT v1 #154787 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KMB
- Type
- protein
- Length
- 435 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear protein STH1/NPS1
- EC
- 3.6.4.12
- UniProt
- P32597
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 110 | 57% helix, 2% strand | P32597 |
| B | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 109 | 60% helix, 2% strand | P32597 |
| C | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 108 | 62% helix, 2% strand | P32597 |
| D | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 108 | 61% helix, 2% strand | P32597 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.84 | 0.94 | 47 | GOL |
| 2 | 289 | 0.84 | 0.95 | 46 | GOL |
| 3 | 84 | 0.34 | 0.75 | 16 | empty |
| 4 | 70 | 0.31 | 0.74 | 14 | empty |
| 5 | 69 | 0.29 | 0.73 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1005 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 961 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 297 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 280 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 189 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 P32597
- Elsewhere: RCSB PDB 6KMB · PDBe 6KMB · UniProt P32597
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