Research workbench
Kick-Off Fab 115 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Analyse Kick-Off Fab 115 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMU
- Type
- protein
- Length
- 1,087 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens
- Molecule
- Fab 115 anti-SIRP-alpha antibody Variable Light Chain; Fab 115 anti-SIRP-alpha antibody…
- UniProt
- P78324
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.55 · 4 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab 115 anti-SIRP-alpha antibody Variable Light Chain | protein | 213 | 7% helix, 49% strand | — |
| H | Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain | protein | 215 | 7% helix, 51% strand | — |
| S, C | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 114 | 3% helix, 43% strand | P78324 |
| B | Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain | protein | 218 | 6% helix, 48% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.72 | 0.79 | 84 | empty |
| 2 | 242 | 0.57 | 0.79 | 36 | empty |
| 3 | 311 | 0.54 | 0.75 | 48 | empty |
| 4 | 206 | 0.51 | 0.76 | 32 | empty |
| 5 | 141 | 0.45 | 0.77 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1793 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1757 Ų buried · 9 hydrogen bonds · protein-protein
- H–S · 669 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 18 hydrogen bonds · protein-protein
- H–B · 339 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6NMU · Kick-off Fab 115 anti-sirp-alpha antibody in complex with sirp-alpha variant 1 · the same entry in another collection · chain C against C, TM-score 1.00
- P78324 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type… · a predicted model of the same protein · chain S against A, TM-score 0.97
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 P78324
- Elsewhere: RCSB PDB 6NMU · PDBe 6NMU · UniProt P78324
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