Research workbench
Non-blocking Fab 218 anti-sirp-alpha antibody in complex with sirp- alpha variant 1
Analyse Non-blocking Fab 218 anti-sirp-alpha antibody in complex with sirp- alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMV
- Type
- protein
- Length
- 527 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein phosphatase non-receptor type substrate 1; Fab 218 anti-sirp-alpha…
- UniProt
- P78324
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 116 | 3% helix, 42% strand | P78324 |
| H | Fab 218 anti-sirp-alpha antibody variable heavy chain | protein | 205 | 7% helix, 48% strand | — |
| L | Fab 218 anti-sirp-alpha antibody variable light chain | protein | 206 | 5% helix, 50% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.57 | 0.74 | 50 | empty |
| 2 | 230 | 0.50 | 0.75 | 31 | empty |
| 3 | 114 | 0.40 | 0.76 | 22 | empty |
| 4 | 56 | 0.40 | 0.81 | 20 | empty |
| 5 | 107 | 0.34 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1626 Ų buried · 9 hydrogen bonds · protein-protein
- S–H · 438 Ų buried · 1 hydrogen bond · protein-protein
- S–L · 381 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6NMV · Non-Blocking Fab 218 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1 · the same entry in another collection · chain S against S, 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 0.96
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 6NMV · PDBe 6NMV · UniProt P78324
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