MolNFT v1 · #158196 · protein
Blocking Fab 136 anti-sirp-alpha antibody in complex with sirp-alpha variant 1
6NMS · Fab 136 anti-sirp-alpha antibody variable light chain: “Blocking Fab 136 anti-sirp-alpha antibody in complex with sirp-alpha variant 1”. X-ray diffraction, 13 pockets (best druggability 0.65). MolNFT v1 #158196 on GenesisL1: 3D…
- PDB
- 6NMS
- Type
- protein
- Length
- 1,094 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 136 anti-sirp-alpha antibody variable light chain; Fab 136 anti-sirp-alpha antibody…
- UniProt
- P78324
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab 136 anti-sirp-alpha antibody variable light chain | protein | 214 | 6% helix, 49% strand | — |
| H | Fab 136 anti-sirp-alpha antibody variable heavy chain | protein | 217 | 7% helix, 52% strand | — |
| S | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 116 | 3% helix, 41% strand | P78324 |
| B | Fab 136 anti-sirp-alpha antibody variable heavy chain | protein | 216 | 7% helix, 52% strand | — |
| C | Tyrosine-protein phosphatase non-receptor type substrate 1 | protein | 117 | 3% helix, 42% strand | P78324 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.65 | 0.95 | 16 | empty |
| 2 | 437 | 0.62 | 0.76 | 39 | empty |
| 3 | 62 | 0.56 | 0.89 | 21 | empty |
| 4 | 259 | 0.53 | 0.76 | 36 | empty |
| 5 | 223 | 0.50 | 0.75 | 33 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1751 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1714 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 12 hydrogen bonds · protein-protein
- H–S · 445 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6NMS · Blocking Fab 136 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 6NMS · PDBe 6NMS · UniProt P78324
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