MolNFT v1 · #143746 · protein
Wt ig-like V domain with phosphatidylserine
6B8O · Triggering receptor expressed on myeloid cells 2: “Wt ig-like V domain with phosphatidylserine”. X-ray diffraction, 4 ligands (PSF, NAG, SO4), 9 pockets (best druggability 0.74). MolNFT v1 #143746 on GenesisL1: 3D structure, binding…
- PDB
- 6B8O
- Type
- protein
- Length
- 643 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triggering receptor expressed on myeloid cells 2
- UniProt
- Q9NZC2
- Ligands
- PSF, NAG, SO4, IOD
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triggering receptor expressed on myeloid cells 2 | protein | 109 | 6% helix, 54% strand | Q9NZC2 |
| B | Triggering receptor expressed on myeloid cells 2 | protein | 107 | 6% helix, 57% strand | Q9NZC2 |
| C | Triggering receptor expressed on myeloid cells 2 | protein | 107 | 6% helix, 55% strand | Q9NZC2 |
| D | Triggering receptor expressed on myeloid cells 2 | protein | 106 | 6% helix, 58% strand | Q9NZC2 |
| E | Triggering receptor expressed on myeloid cells 2 | protein | 105 | 6% helix, 56% strand | Q9NZC2 |
| F | Triggering receptor expressed on myeloid cells 2 | protein | 109 | 6% helix, 56% strand | Q9NZC2 |
Ligands and binding sites
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · 3 copies · chains B, E, C, F, A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D, B, E, C, F
- SO4 · Sulfate ion · ion · 11 copies · chains A, F, D, E, B, C
- IOD · Iodide ion · ion · 7 copies · chains A, C, B, E
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, F, D, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.74 | 0.80 | 67 | empty |
| 2 | 285 | 0.66 | 0.82 | 35 | EDO |
| 3 | 353 | 0.65 | 0.80 | 34 | empty |
| 4 | 455 | 0.64 | 0.77 | 38 | EDO |
| 5 | 58 | 0.31 | 0.76 | 16 | SO4 |
Interfaces
9 interfaces between chains.
- A–C · 386 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 329 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 Q9NZC2
- Elsewhere: RCSB PDB 6B8O · PDBe 6B8O · UniProt Q9NZC2
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