MolNFT v1 · #118616 · protein
Human T-cell immunoglobulin and mucin domain protein 4 (htim-4) complex with phosphoserine
5F7H · T-cell immunoglobulin and mucin domain-containing protein 4: “Human T-cell immunoglobulin and mucin domain protein 4 (htim-4) complex with phosphoserine”. X-ray diffraction, 2 ligands (SEP, CA), 5 pockets (best druggability 0.81).…
- PDB
- 5F7H
- Type
- protein
- Length
- 674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell immunoglobulin and mucin domain-containing protein 4
- UniProt
- Q96H15
- Ligands
- SEP, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, D, E | T-cell immunoglobulin and mucin domain-containing protein 4 | protein | 113 | 5% helix, 44% strand | Q96H15 |
| C, F | T-cell immunoglobulin and mucin domain-containing protein 4 | protein | 111 | 5% helix, 44% strand | Q96H15 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 6 copies · chains B, A, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.81 | 0.83 | 85 | CA, SEP |
| 2 | 389 | 0.70 | 0.82 | 40 | SEP |
| 3 | 685 | 0.67 | 0.76 | 60 | SEP |
| 4 | 222 | 0.52 | 0.76 | 27 | empty |
| 5 | 185 | 0.50 | 0.77 | 23 | empty |
Interfaces
11 interfaces between chains.
- C–D · 804 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 779 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 538 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 510 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 307 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5F7H · Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) complex with phosphoserine · the same entry in another collection · chain F against F, TM-score 1.00
- Q96H15 · AlphaFold monomer V2.0 prediction for T-cell immunoglobulin and mucin domain-containing… · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q96H15
- Elsewhere: RCSB PDB 5F7H · PDBe 5F7H · UniProt Q96H15
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