5CBA: 3B4
3B4 in complex with CXCL13 - 3B4-CXCL13. Determined by X-ray diffraction at 2.5 Å resolution. Released 4 Nov 2015.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 4,747
- Mol. weight
- 75.77 kDa
- Released
- 4 Nov 2015
Explore 5CBA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5CBA contains 14 α-helices and 67 β-strands across 6 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, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 1 |
| β-strand | 3-6 | 4 | 2 |
| α-helix | 7-9 | 3 | |
| β-strand | 10-12 | 3 | 3 |
| β-strand | 18-25 | 8 | 2 |
| β-strand | 33-39 | 7 | 3 |
| β-strand | 45-52 | 8 | 3 |
| β-strand | 56-59 | 4 | 3 |
| α-helix | 61-63 | 3 | |
| β-strand | 64 | 1 | 2 |
| β-strand | 67-72 | 6 | 2 |
| β-strand | 77-82 | 6 | 2 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 3 |
| β-strand | 97-100 | 4 | 4 |
| β-strand | 100C-100F | 4 | 4 |
| β-strand | 102-103 | 2 | 3 |
| β-strand | 107-111 | 5 | 3 |
Chain B: 3 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3 | 1 | |
| β-strand | 4 | 1 | 5 |
| β-strand | 5 | 1 | 6 |
| β-strand | 9-13 | 4 | 7 |
| β-strand | 19-24 | 6 | 6 |
| β-strand | 33-38 | 6 | 7 |
| β-strand | 45-48 | 4 | 7 |
| β-strand | 49 | 1 | 8 |
| β-strand | 53 | 1 | 8 |
| β-strand | 62-67 | 6 | 6 |
| β-strand | 70-75 | 6 | 6 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-91 | 7 | 7 |
| β-strand | 96-98 | 3 | 7 |
| β-strand | 99 | 1 | 5 |
| β-strand | 102-106 | 5 | 7 |
| α-helix | 106A-107 | 2 | |
Chain C: 3 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 1 |
| β-strand | 3-6 | 4 | 9 |
| α-helix | 7-9 | 3 | |
| β-strand | 10-12 | 3 | 10 |
| β-strand | 18-25 | 8 | 9 |
| β-strand | 33-39 | 7 | 10 |
| β-strand | 45-52 | 8 | 10 |
| β-strand | 56-59 | 4 | 10 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 9 |
| β-strand | 77-82 | 6 | 9 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 10 |
| β-strand | 97-99 | 3 | 11 |
| β-strand | 100D-100F | 3 | 11 |
| β-strand | 102-103 | 2 | 10 |
| β-strand | 107-111 | 5 | 10 |
Chain D: 1 helix, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 12 |
| β-strand | 5 | 1 | 13 |
| β-strand | 9-13 | 4 | 14 |
| β-strand | 19-24 | 6 | 13 |
| β-strand | 33-38 | 6 | 14 |
| β-strand | 45-48 | 4 | 14 |
| β-strand | 49 | 1 | 15 |
| β-strand | 53 | 1 | 15 |
| β-strand | 62-67 | 6 | 13 |
| β-strand | 70-75 | 6 | 13 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-91 | 7 | 14 |
| β-strand | 96-98 | 3 | 14 |
| β-strand | 99 | 1 | 12 |
| β-strand | 102-106 | 5 | 14 |
Chain E: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 4 |
| α-helix | 21-23 | 3 | |
| β-strand | 24-30 | 7 | 4 |
| β-strand | 33 | 1 | 16 |
| β-strand | 36 | 1 | 16 |
| β-strand | 40-45 | 6 | 4 |
| β-strand | 50-53 | 4 | 4 |
| α-helix | 58-66 | 9 | |
Chain F: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 11 |
| α-helix | 21-23 | 3 | |
| β-strand | 24-30 | 7 | 11 |
| β-strand | 40-45 | 6 | 11 |
| β-strand | 50-53 | 4 | 11 |
| α-helix | 58-68 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 3b4 heavy chain | A, C | protein | 142 | Homo sapiens | A0A0B4J2H0 (AlphaFold model) |
| 3b4 light chain | B, D | protein | 117 | Homo sapiens | P01704 (AlphaFold model) |
| C-X-C motif chemokine 13 | E, F | protein | 88 | Homo sapiens | O43927 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>5CBA_1 3b4 heavy chain (chains A, C)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCAREPDYYDSSGYYPIDAFDIWGQG
TTVTVSSGGGGSGGGGSGGGGS
Sequence of entity 2 (B, D), FASTA
>5CBA_2 3b4 light chain (chains B, D)
QSALTQPASVSASPGQSITISCTGTSSDVGAYDWVSWYQQHPGKAPKLLIFDVNNRPSGV
SHRFSGSKSGNTASLTISGLQAEDEADYYCSSYTRRDTYVFGTGTKVTVLGENLYFQ
Sequence of entity 3 (E, F), FASTA
>5CBA_3 C-X-C motif chemokine 13 (chains E, F)
MVLEVYYTSLRCRCVQESSVFIPRRFIDRIQILPRGNGCPRKEIIVWKKNKSIVCVDPQA
EWIQRMMEVLRKRSSSTLPVPVFKRKIP
Primary citation
A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv). Tu, C., Terraube, V., Tam, A.S. et al. J Biol Chem (2016) 291:1267-1276. DOI 10.1074/jbc.M115.688010 · PubMed
Other PDB entries of the same protein (UniProt A0A0B4J2H0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5C2B 1.4 Å, anti-CXCL13 parental scFv - 3B4
- 5C6W 1.54 Å, anti-CXCL13 scFv - E10
- 5WKZ 1.85 Å, VH1-69 germline antibody predicted from CR6261
- 5CBE 2.4 Å, E10 in complex with CXCL13
Browse structure collections
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