6VGJ: N-terminal variant of CXCL13
N-terminal variant of CXCL13. Determined by X-ray diffraction at 2.52 Å resolution. Released 7 Oct 2020.
- Method
- X-ray diffraction
- Resolution
- 2.52 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 4,249
- Mol. weight
- 71.78 kDa
- Released
- 7 Oct 2020
Explore 6VGJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6VGJ contains 16 α-helices and 39 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 1 |
| β-strand | 15-17 | 3 | 1 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 1 |
| β-strand | 42-47 | 6 | 1 |
| β-strand | 52-55 | 4 | 1 |
| α-helix | 60-72 | 13 | |
| α-helix | 78-80 | 3 | |
Chain B: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 2 |
| β-strand | 15-17 | 3 | 2 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 2 |
| β-strand | 42-47 | 6 | 2 |
| β-strand | 52-55 | 4 | 2 |
| α-helix | 60-71 | 12 | |
Chain C: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 1 |
| β-strand | 15-17 | 3 | 1 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 1 |
| β-strand | 35 | 1 | 3 |
| β-strand | 38 | 1 | 3 |
| β-strand | 42-47 | 6 | 1 |
| β-strand | 52-55 | 4 | 1 |
| α-helix | 60-71 | 12 | |
Chain D: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 1 |
| β-strand | 15-17 | 3 | 1 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 1 |
| β-strand | 35 | 1 | 4 |
| β-strand | 38 | 1 | 4 |
| β-strand | 42-47 | 6 | 1 |
| β-strand | 52-55 | 4 | 1 |
| α-helix | 60-72 | 13 | |
Chain E: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 5 |
| β-strand | 15-17 | 3 | 5 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 5 |
| β-strand | 42-47 | 6 | 5 |
| β-strand | 52-55 | 4 | 5 |
| α-helix | 60-70 | 11 | |
Chain F: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 6 |
| β-strand | 15-17 | 3 | 6 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 6 |
| β-strand | 42-47 | 6 | 6 |
| β-strand | 52-55 | 4 | 6 |
| α-helix | 60-71 | 12 | |
| α-helix | 72-74 | 3 | |
Chain G: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 5 |
| β-strand | 15-17 | 3 | 5 |
| α-helix | 23-25 | 3 | |
| β-strand | 26-32 | 7 | 5 |
| β-strand | 42-47 | 6 | 5 |
| β-strand | 52-55 | 4 | 5 |
| α-helix | 60-72 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| C-X-C motif chemokine 13 | A, B, C, D, E, F, G | protein | 86 | Homo sapiens | O43927 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G), FASTA
>6VGJ_1 C-X-C motif chemokine 13 (chains A, B, C, D, E, F, G)
MEVYYTSLRCRCVQESSVFIPRRFIDRIQILPRGNGCPRKEIIVWKKNKSIVCVDPQAEW
IQRMMEVLRKRSSSTLPVPVFKRKIP
Primary citation
The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity. Rosenberg Jr., E.M., Herrington, J., Rajasekaran, D. et al. Acta Crystallogr D Struct Biol (2020) 76:1033-1049. DOI 10.1107/S2059798320011687 · PubMed
Other PDB entries of the same protein (UniProt O43927 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7JNY 1.88 Å, Crystal structure of CXCL13
- 5CBE 2.4 Å, E10 in complex with CXCL13
- 5CBA 2.5 Å, 3B4 in complex with CXCL13 - 3B4-CXCL13
Browse structure collections
About this viewer
MolViewer shows 6VGJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.