MolNFT v1 · #94715 · protein
Bel beta-trefoil complex with T-antigen
4I4Y: “Bel beta-trefoil complex with T-antigen”. X-ray diffraction, 3 ligands (SER, A2G, GAL), 3 pockets (best druggability 0.77). MolNFT v1 #94715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I4Y
- Type
- protein
- Length
- 584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bel beta-trefoil
- Ligands
- SER, A2G, GAL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bel beta-trefoil | protein | 146 | 8% helix, 38% strand | — |
Ligands and binding sites
- SER · Serine · ligand · 6 copies · chains B, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 6 copies · chains B, C, D
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.77 | 0.79 | 115 | empty |
| 2 | 153 | 0.74 | 0.92 | 35 | empty |
| 3 | 63 | 0.35 | 0.78 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 853 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 793 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 293 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4I4Y · BEL beta-trefoil complex with T-Antigen · 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
- Elsewhere: RCSB PDB 4I4Y · PDBe 4I4Y
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