MolNFT v1 · #106186 · protein
Crystal structure of the Fab complexed with antigen ASF1P, northeast structural genomics consortium (nesg) target PDR16
4RRP · Fab antibody, light chain: “Crystal structure of the Fab complexed with antigen ASF1P, northeast structural genomics consortium (nesg)…”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #106186 on GenesisL1: 3D…
- 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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