MolNFT v1 · #163904 · protein
Engbf darpin fusion 4B D12
6SH9 · Endo-alpha-N-ACETYLGALACTOSAMINIDASE,DARPIN 4B D12: “Engbf darpin fusion 4B D12”. X-ray diffraction, 1 ligand (MN), 15 pockets (best druggability 0.81). MolNFT v1 #163904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SH9
- Type
- protein
- Length
- 1,349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-alpha-N-ACETYLGALACTOSAMINIDASE,DARPIN 4B D12; Envelope glycoprotein GP160
- EC
- 3.2.1.97
- UniProt
- Q3T552, P05877
- Ligands
- MN
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Endo-alpha-N-ACETYLGALACTOSAMINIDASE,DARPIN 4B D12 (EC 3.2.1.97) | protein | 1339 | 21% helix, 31% strand | Q3T552 |
| E | Envelope glycoprotein GP160 | protein | 10 | 0% helix, 20% strand | P05877 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.81 | 0.96 | 50 | empty |
| 2 | 70 | 0.75 | 0.99 | 24 | empty |
| 3 | 820 | 0.72 | 0.77 | 81 | empty |
| 4 | 230 | 0.52 | 0.76 | 36 | empty |
| 5 | 144 | 0.52 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- B–E · 486 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6SH9 · EngBF DARPin Fusion 4b D12 · the same entry in another collection · chain B against B, 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 Q3T552
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 6SH9 · PDBe 6SH9 · UniProt Q3T552 · UniProt P05877
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