Research workbench
Development and preclinical characterization of a humanized antibody targeting CXCL12
Analyse Development and preclinical characterization of a humanized antibody targeting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LMQ
- Type
- protein
- Length
- 956 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromal cell-derived factor 1; HU30D8 Fab heavy chain; HU30D8 Fab light chain
- UniProt
- P48061
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Stromal cell-derived factor 1 | protein | 55 | 24% helix, 27% strand | P48061 |
| E | HU30D8 Fab heavy chain | protein | 195 | 3% helix, 50% strand | — |
| F | Stromal cell-derived factor 1 | protein | 58 | 19% helix, 29% strand | P48061 |
| H | HU30D8 Fab heavy chain | protein | 220 | 5% helix, 50% strand | — |
| I, L | HU30D8 Fab light chain | protein | 214 | 5% helix, 45% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.61 | 0.74 | 63 | empty |
| 2 | 258 | 0.56 | 0.77 | 39 | empty |
| 3 | 310 | 0.55 | 0.75 | 36 | empty |
| 4 | 86 | 0.34 | 0.75 | 18 | empty |
| 5 | 95 | 0.34 | 0.73 | 15 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1851 Ų buried · 15 hydrogen bonds · protein-protein
- E–I · 1776 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 880 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 506 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 499 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4LMQ · Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12 · the same entry in another collection · chain L against L, TM-score 1.00
- P48061 · AlphaFold monomer V2.0 prediction for stromal cell-derived factor 1 (P48061) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 P48061
- Elsewhere: RCSB PDB 4LMQ · PDBe 4LMQ · UniProt P48061
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