MolNFT v1 · #158197 · protein
Non-blocking Fab 3 anti-sirp-alpha antibody in complex with sirp-alpha variant 1
6NMT · Fab 3 anti-sirp-alpha antibody variable light chain: “Non-blocking Fab 3 anti-sirp-alpha antibody in complex with sirp-alpha variant 1”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #158197 on GenesisL1: 3D…
- PDB
- 6NMT
- Type
- protein
- Length
- 537 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 3 anti-sirp-alpha antibody variable light chain; Fab 3 anti-sirp-alpha antibody…
- UniProt
- P78324
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab 3 anti-sirp-alpha antibody variable light chain | protein | 208 | 6% helix, 52% strand | — |
| B | Fab 3 anti-sirp-alpha antibody variable heavy chain | protein | 214 | 10% helix, 52% strand | — |
| C | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 115 | 3% helix, 41% strand | P78324 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.62 | 0.75 | 65 | empty |
| 2 | 111 | 0.38 | 0.75 | 24 | empty |
| 3 | 107 | 0.37 | 0.75 | 15 | empty |
| 4 | 60 | 0.37 | 0.79 | 17 | empty |
| 5 | 96 | 0.34 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1745 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6NMT · Non-Blocking Fab 3 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1 · the same entry in another collection · chain A against A, 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 C 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 6NMT · PDBe 6NMT · UniProt P78324
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