Research workbench
X-ray crystallographic study of piydin, which contains the truncation determinants of binding pi and N, bound to ROAB13, a CCR5 antibody
Analyse X-ray crystallographic study of piydin, which contains the truncation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NW3
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody ROAB13 heavy chain; Antibody ROAB13 light chain; Region from C-C chemokine…
- UniProt
- P51681
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody ROAB13 heavy chain | protein | 218 | 4% helix, 48% strand | — |
| L | Antibody ROAB13 light chain | protein | 214 | 3% helix, 40% strand | — |
| A | Region from C-C chemokine receptor type 5 N-terminal domain | protein | 6 | 0% helix, 0% strand | P51681 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.62 | 0.75 | 54 | empty |
| 2 | 153 | 0.48 | 0.77 | 18 | empty |
| 3 | 72 | 0.44 | 0.81 | 20 | empty |
| 4 | 78 | 0.36 | 0.76 | 12 | empty |
| 5 | 86 | 0.35 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1842 Ų buried · 21 hydrogen bonds · protein-protein
- L–A · 276 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7NW3 · X-ray crystallographic study of PIYDIN, which contains the truncation determinants of… · the same entry in another collection · chain H against H, TM-score 1.00
- P51681 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 5 (P51681) · a predicted model of the same protein · chain A against A, TM-score 0.40
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 P51681
- Elsewhere: RCSB PDB 7NW3 · PDBe 7NW3 · UniProt P51681
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