Research workbench
Blocking Fab 119 anti-sirp-alpha antibody in complex with sirp-alpha variant 1
Analyse Blocking Fab 119 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
- 6NMR
- Type
- protein
- Length
- 2,171 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 119 anti-sirp-alpha antibody variable light chain; Fab 119 anti-sirp-alpha antibody…
- UniProt
- P78324
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 9 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, G | Fab 119 anti-sirp-alpha antibody variable light chain | protein | 214 | 6% helix, 50% strand | — |
| H | Fab 119 anti-sirp-alpha antibody variable heavy chain | protein | 218 | 5% helix, 57% strand | — |
| S | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 113 | 3% helix, 38% strand | P78324 |
| B, K | Fab 119 anti-sirp-alpha antibody variable light chain | protein | 213 | 7% helix, 50% strand | — |
| A | Fab 119 anti-sirp-alpha antibody variable heavy chain | protein | 217 | 6% helix, 55% strand | — |
| E | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 112 | 3% helix, 38% strand | P78324 |
| F | Fab 119 anti-sirp-alpha antibody variable heavy chain | protein | 215 | 7% helix, 52% strand | — |
| I, M | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 112 | 3% helix, 32% strand | P78324 |
| J | Fab 119 anti-sirp-alpha antibody variable heavy chain | protein | 218 | 1% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.73 | 0.89 | 39 | empty |
| 2 | 998 | 0.72 | 0.76 | 72 | empty |
| 3 | 262 | 0.70 | 0.85 | 33 | empty |
| 4 | 368 | 0.70 | 0.82 | 43 | empty |
| 5 | 1044 | 0.69 | 0.74 | 102 | empty |
Interfaces
22 interfaces between chains.
- L–H · 1964 Ų buried · 15 hydrogen bonds · protein-protein
- G–F · 1825 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1814 Ų buried · 10 hydrogen bonds · protein-protein
- K–J · 1720 Ų buried · 11 hydrogen bonds · protein-protein
- H–S · 919 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6NMR · Blocking Fab 119 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1 · the same entry in another collection · chain M against M, 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 P78324
- Elsewhere: RCSB PDB 6NMR · PDBe 6NMR · UniProt P78324
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