MolNFT v1 · #162416 · protein
Cryo-EM structure of the human brisc-SHMT2 complex
6R8F · Lys-63-specific deubiquitinase BRCC36: “Cryo-EM structure of the human brisc-SHMT2 complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.76). MolNFT v1 #162416 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6R8F
- Type
- protein
- Length
- 2,164 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lys-63-specific deubiquitinase BRCC36; Brisc complex subunit abraxas 2; Serine…
- EC
- 3.4.19.-, 2.1.2.1
- UniProt
- P46736, Q15018, P34897, Q9NXR7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 4 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lys-63-specific deubiquitinase BRCC36 (EC 3.4.19.-) | protein | 238 | 39% helix, 21% strand | P46736 |
| B, D | Brisc complex subunit abraxas 2 | protein | 230 | 33% helix, 17% strand | Q15018 |
| K, L | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 404 | 39% helix, 13% strand | P34897 |
| E, G | Brisc and BRCA1-a complex member 2,BRCC45 (bre, brisc and BRCA1-a complex member 2) | protein | 210 | 24% helix, 15% strand | Q9NXR7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.76 | 0.79 | 112 | empty |
| 2 | 1180 | 0.75 | 0.78 | 127 | empty |
| 3 | 583 | 0.73 | 0.80 | 52 | empty |
| 4 | 490 | 0.72 | 0.82 | 101 | empty |
| 5 | 55 | 0.69 | 0.96 | 18 | empty |
Interfaces
17 interfaces between chains.
- A–B · 4267 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 4189 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 2558 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1289 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 1241 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6R8F · Cryo-EM structure of the Human BRISC-SHMT2 complex · the same entry in another collection · chain G against G, TM-score 1.00
- P46736 · AlphaFold monomer V2.0 prediction for lys-63-specific deubiquitinase BRCC36 (P46736) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · a predicted model of the same protein · chain K against A, TM-score 0.97
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 P46736
- Every structure of UniProt Q15018
- Every structure of UniProt P34897
- Every structure of UniProt Q9NXR7
- Elsewhere: RCSB PDB 6R8F · PDBe 6R8F · UniProt P46736 · UniProt Q15018 · UniProt P34897 · UniProt Q9NXR7
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