Research workbench
Crystal structure of mbp-TREM2 ig domain fusion with fragment, 2-((4- BROMOPHENYL)AMINO)ETHAN-1-ol
Analyse Crystal structure of mbp-TREM2 ig domain fusion with fragment, 2-((4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XDS
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar ABC transporter substrate-binding PROTEIN,TRIGGERING receptor expressed on myeloid…
- UniProt
- A0A0F8NYV9, Q9NZC2
- Ligands
- V5S, GLC
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar ABC transporter substrate-binding PROTEIN,TRIGGERING receptor expressed on myeloid cells 2 | protein | 485 | 35% helix, 29% strand | A0A0F8NYV9, Q9NZC2 |
Ligands and binding sites
- V5S · 2-[(4-bromophenyl)amino]ethan-1-ol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
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 | 356 | 0.75 | 0.85 | 30 | GLC |
| 2 | 889 | 0.74 | 0.78 | 61 | DMS |
| 3 | 80 | 0.49 | 0.84 | 19 | empty |
| 4 | 119 | 0.38 | 0.74 | 21 | empty |
| 5 | 60 | 0.29 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6XDS · Crystal structure of MBP-TREM2 Ig domain fusion with fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZC2 · AlphaFold monomer V2.0 prediction for triggering receptor expressed on myeloid cells 2… · a predicted model of the same protein · chain A against A, TM-score 0.25
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 A0A0F8NYV9
- Every structure of UniProt Q9NZC2
- Elsewhere: RCSB PDB 6XDS · PDBe 6XDS · UniProt A0A0F8NYV9 · UniProt Q9NZC2
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