MolNFT v1 · #176704 · protein
Crystal structure of anti-ctla-4 vh domain in complex with human ctla- 4
7DV4 · Cytotoxic T-lymphocyte protein 4: “Crystal structure of anti-ctla-4 vh domain in complex with human ctla- 4”. X-ray diffraction, 9 pockets (best druggability 0.81). MolNFT v1 #176704 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DV4
- Type
- protein
- Length
- 930 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic T-lymphocyte protein 4; 4003-1(VH)
- UniProt
- P16410
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxic T-lymphocyte protein 4 | protein | 115 | 3% helix, 57% strand | P16410 |
| B, F | 4003-1(VH) | protein | 119 | 5% helix, 47% strand | — |
| C | Cytotoxic T-lymphocyte protein 4 | protein | 113 | 0% helix, 58% strand | P16410 |
| D | 4003-1(VH) | protein | 117 | 8% helix, 49% strand | — |
| E | Cytotoxic T-lymphocyte protein 4 | protein | 116 | 3% helix, 64% strand | P16410 |
| G | Cytotoxic T-lymphocyte protein 4 | protein | 111 | 3% helix, 57% strand | P16410 |
| H | 4003-1(VH) | protein | 120 | 5% helix, 48% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.81 | 0.83 | 82 | empty |
| 2 | 581 | 0.71 | 0.80 | 59 | EDO |
| 3 | 98 | 0.69 | 0.92 | 24 | empty |
| 4 | 95 | 0.68 | 0.91 | 23 | empty |
| 5 | 557 | 0.65 | 0.76 | 54 | empty |
Interfaces
14 interfaces between chains.
- C–D · 818 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 753 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 751 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 621 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7DV4 · Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4 · the same entry in another collection · chain H against H, TM-score 1.00
- P16410 · AlphaFold monomer V2.0 prediction for cytotoxic T-lymphocyte protein 4 (P16410) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 P16410
- Elsewhere: RCSB PDB 7DV4 · PDBe 7DV4 · UniProt P16410
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