Research workbench
Crystal structure of rhesus TRIM5ALPHA PRY/SPRY domain
Analyse Crystal structure of rhesus TRIM5ALPHA PRY/SPRY domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B3N
- Type
- protein
- Length
- 1,113 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, tripartite motif- containing protein 5
- UniProt
- P0AEX9, Q0PF16
- Ligands
- GLC
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, tripartite motif- containing protein 5 | protein | 557 | 33% helix, 27% strand | P0AEX9, Q0PF16 |
| B | Maltose-binding periplasmic protein, tripartite motif- containing protein 5 | protein | 556 | 33% helix, 27% strand | P0AEX9, Q0PF16 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.76 | 0.79 | 94 | GLC |
| 2 | 678 | 0.75 | 0.81 | 48 | GLC |
| 3 | 473 | 0.60 | 0.75 | 54 | empty |
| 4 | 291 | 0.54 | 0.75 | 34 | empty |
| 5 | 168 | 0.49 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4B3N · Crystal structure of rhesus TRIM5alpha PRY/SPRY domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q0PF16 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 5 (Q0PF16) · a predicted model of the same protein · chain A against A, TM-score 0.36
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 P0AEX9
- Every structure of UniProt Q0PF16
- Elsewhere: RCSB PDB 4B3N · PDBe 4B3N · UniProt P0AEX9 · UniProt Q0PF16
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