Research workbench
Crystal structure of wild-type ig-like domain
Analyse Crystal structure of wild-type ig-like domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UD7
- 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
- NAG, IOD, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triggering receptor expressed on myeloid cells 2 | protein | 109 | 6% helix, 52% strand | Q9NZC2 |
| B | Triggering receptor expressed on myeloid cells 2 | protein | 107 | 6% helix, 58% strand | Q9NZC2 |
| C | Triggering receptor expressed on myeloid cells 2 | protein | 107 | 6% helix, 55% strand | Q9NZC2 |
| D, E | Triggering receptor expressed on myeloid cells 2 | protein | 105 | 6% helix, 56% strand | Q9NZC2 |
| F | Triggering receptor expressed on myeloid cells 2 | protein | 110 | 5% helix, 55% strand | Q9NZC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, D, B, E, C, F
- IOD · Iodide ion · ion · 5 copies · chains B, C, E
- SO4 · Sulfate ion · ion · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.76 | 0.78 | 72 | empty |
| 2 | 368 | 0.66 | 0.80 | 36 | empty |
| 3 | 376 | 0.66 | 0.80 | 38 | empty |
| 4 | 381 | 0.66 | 0.79 | 37 | empty |
| 5 | 75 | 0.32 | 0.75 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 381 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 360 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 340 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 314 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 5UD7 · PDBe 5UD7 · UniProt Q9NZC2
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