MolNFT v1 · #116727 · protein
X-ray structure of the Fab fragment of the anti tau antibody RB86 in complex with the phosphorylated tau peptide (416-430)
5DMG · RB86 antibody Fab fragment heavy chain: “X-ray structure of the Fab fragment of the anti tau antibody RB86 in complex with the phosphorylated tau…”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1 #116727 on…
- PDB
- 5DMG
- Type
- protein
- Length
- 1,278 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RB86 antibody Fab fragment heavy chain; RB86 antibody Fab fragment light chain…
- UniProt
- B4DSE3
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C | RB86 antibody Fab fragment heavy chain | protein | 202 | 6% helix, 51% strand | — |
| L | RB86 antibody Fab fragment light chain | protein | 216 | 6% helix, 52% strand | — |
| D | RB86 antibody Fab fragment light chain | protein | 217 | 6% helix, 51% strand | — |
| E | RB86 antibody Fab fragment heavy chain | protein | 198 | 3% helix, 54% strand | — |
| F | RB86 antibody Fab fragment light chain | protein | 215 | 5% helix, 47% strand | — |
| Z | Microtubule-associated protein | protein | 9 | 0% helix, 0% strand | B4DSE3 |
| P | Microtubule-associated protein | protein | 12 | 0% helix, 0% strand | B4DSE3 |
| X | Microtubule-associated protein | protein | 7 | 0% helix, 0% strand | B4DSE3 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.77 | 0.82 | 79 | empty |
| 2 | 543 | 0.61 | 0.74 | 65 | empty |
| 3 | 398 | 0.59 | 0.76 | 45 | empty |
| 4 | 151 | 0.55 | 0.81 | 37 | empty |
| 5 | 57 | 0.46 | 0.85 | 21 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1601 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1579 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1572 Ų buried · 17 hydrogen bonds · protein-protein
- H–P · 469 Ų buried · 7 hydrogen bonds · protein-protein
- D–Z · 391 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 modified (disulfide, phosphorylation).
Compared structures
- 5DMG · X-ray structure of the Fab fragment of the anti tau antibody RB86 in complex with the… · the same entry in another collection · chain H against H, 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 B4DSE3
- Elsewhere: RCSB PDB 5DMG · PDBe 5DMG · UniProt B4DSE3
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