Research workbench
Crystal structure of the Fab complexed with antigen ASF1P, northeast structural genomics consortium (nesg) target PDR16
Analyse Crystal structure of the Fab complexed with antigen ASF1P, northeast structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RRP
- Type
- protein
- Length
- 3,503 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab antibody, light chain; Fab antibody, heavy chain; Antigen ASF1P
- UniProt
- E7KE71
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 17 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab antibody, light chain | protein | 213 | 6% helix, 51% strand | — |
| G | Fab antibody, heavy chain | protein | 219 | 7% helix, 50% strand | — |
| B | Fab antibody, light chain | protein | 216 | 6% helix, 50% strand | — |
| H | Fab antibody, heavy chain | protein | 221 | 5% helix, 49% strand | — |
| C | Fab antibody, light chain | protein | 212 | 6% helix, 53% strand | — |
| I | Fab antibody, heavy chain | protein | 220 | 5% helix, 48% strand | — |
| D, F | Fab antibody, light chain | protein | 214 | 6% helix, 51% strand | — |
| J | Fab antibody, heavy chain | protein | 222 | 8% helix, 49% strand | — |
| E | Fab antibody, light chain | protein | 214 | 3% helix, 51% strand | — |
| K | Fab antibody, heavy chain | protein | 214 | 6% helix, 49% strand | — |
| L | Fab antibody, heavy chain | protein | 214 | 3% helix, 44% strand | — |
| M | Antigen ASF1P | protein | 153 | 9% helix, 50% strand | E7KE71 |
| N | Antigen ASF1P | protein | 152 | 7% helix, 49% strand | E7KE71 |
| O | Antigen ASF1P | protein | 153 | 7% helix, 50% strand | E7KE71 |
| P | Antigen ASF1P | protein | 156 | 9% helix, 49% strand | E7KE71 |
| Q | Antigen ASF1P | protein | 153 | 6% helix, 49% strand | E7KE71 |
| R | Antigen ASF1P | protein | 143 | 6% helix, 55% strand | E7KE71 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.70 | 0.76 | 93 | empty |
| 2 | 471 | 0.70 | 0.81 | 44 | empty |
| 3 | 467 | 0.68 | 0.79 | 53 | empty |
| 4 | 692 | 0.68 | 0.76 | 57 | empty |
| 5 | 652 | 0.65 | 0.75 | 83 | empty |
Interfaces
37 interfaces between chains.
- B–H · 1979 Ų buried · 17 hydrogen bonds · protein-protein
- D–J · 1960 Ų buried · 19 hydrogen bonds · protein-protein
- F–L · 1910 Ų buried · 17 hydrogen bonds · protein-protein
- C–I · 1861 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1848 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4RRP · Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics… · the same entry in another collection · chain A against A, TM-score 1.00
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 E7KE71
- Elsewhere: RCSB PDB 4RRP · PDBe 4RRP · UniProt E7KE71
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