Research workbench
3B4 in complex with CXCL13 - 3B4-CXCL13
Analyse 3B4 in complex with CXCL13 - 3B4-CXCL13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CBA
- Type
- protein
- Length
- 602 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3B4 heavy chain; 3B4 light chain; C-X-C motif chemokine 13
- UniProt
- A0A0B4J2H0, P04209, O43927
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3B4 heavy chain | protein | 127 | 5% helix, 56% strand | A0A0B4J2H0 |
| B | 3B4 light chain | protein | 112 | 3% helix, 46% strand | P04209 |
| D | 3B4 light chain | protein | 111 | 3% helix, 47% strand | P04209 |
| E | C-X-C motif chemokine 13 | protein | 61 | 20% helix, 33% strand | O43927 |
| F | C-X-C motif chemokine 13 | protein | 64 | 22% helix, 28% strand | O43927 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, E, C, D, F
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.77 | 0.79 | 130 | empty |
| 2 | 77 | 0.70 | 0.95 | 20 | EDO |
| 3 | 67 | 0.55 | 0.88 | 20 | EDO |
| 4 | 206 | 0.53 | 0.78 | 33 | empty |
| 5 | 174 | 0.49 | 0.77 | 31 | empty |
Interfaces
9 interfaces between chains.
- C–D · 854 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 831 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 791 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 787 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5CBA · 3B4 in complex with CXCL13 - 3B4-CXCL13 · the same entry in another collection · chain F against F, TM-score 1.00
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain A against H, TM-score 0.89
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain A against H, TM-score 0.89
- O43927 · AlphaFold monomer V2.0 prediction for C-X-C motif chemokine 13 (O43927) · a predicted model of the same protein · chain E against A, TM-score 0.88
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 A0A0B4J2H0
- Every structure of UniProt P04209
- Every structure of UniProt O43927
- Elsewhere: RCSB PDB 5CBA · PDBe 5CBA · UniProt A0A0B4J2H0 · UniProt P04209 · UniProt O43927
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