3HP3: CXCL12
Crystal structure of CXCL12. Determined by X-ray diffraction at 2.2 Å resolution. Released 26 Jan 2010.
- Method
- X-ray diffraction
- Resolution
- 2.2 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 5,222
- Mol. weight
- 82.17 kDa
- Ligands
- AU
- Released
- 26 Jan 2010
Explore 3HP3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3HP3 contains 23 α-helices and 61 β-strands across 10 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, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 1 |
| β-strand | 11 | 1 | 2 |
| β-strand | 15 | 1 | 3 |
| α-helix | 20-22 | 3 | |
| β-strand | 25-29 | 5 | 3 |
| β-strand | 37-41 | 5 | 3 |
| β-strand | 48-51 | 4 | 3 |
| α-helix | 52 | 1 | |
| α-helix | 56-63 | 8 | |
Chain B: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 2 |
| β-strand | 11 | 1 | 1 |
| β-strand | 15 | 1 | 4 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-28 | 6 | 4 |
| β-strand | 38-42 | 5 | 4 |
| β-strand | 48-51 | 4 | 4 |
| α-helix | 56-62 | 7 | |
Chain C: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 5 |
| β-strand | 11 | 1 | 6 |
| β-strand | 15 | 1 | 7 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-29 | 7 | 7 |
| β-strand | 37-42 | 6 | 7 |
| β-strand | 48-51 | 4 | 7 |
| α-helix | 52 | 1 | |
| α-helix | 56-63 | 8 | |
Chain D: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 8 |
| β-strand | 11 | 1 | 9 |
| α-helix | 14 | 1 | |
| β-strand | 15 | 1 | 10 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-29 | 7 | 10 |
| β-strand | 37-42 | 6 | 10 |
| β-strand | 48-51 | 4 | 10 |
| α-helix | 56-65 | 10 | |
Chain E: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 11 |
| β-strand | 11 | 1 | 12 |
| β-strand | 15 | 1 | 13 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-29 | 7 | 13 |
| β-strand | 37-42 | 6 | 13 |
| β-strand | 48-51 | 4 | 13 |
| α-helix | 56-62 | 7 | |
Chain F: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 9 |
| β-strand | 11 | 1 | 8 |
| β-strand | 15 | 1 | 14 |
| α-helix | 20-22 | 3 | |
| β-strand | 23 | 1 | 15 |
| β-strand | 27-29 | 3 | 16 |
| β-strand | 37-41 | 5 | 16 |
| β-strand | 42 | 1 | 15 |
| β-strand | 48-50 | 3 | 16 |
| β-strand | 51 | 1 | 14 |
| α-helix | 56-65 | 10 | |
Chain G: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 12 |
| β-strand | 11 | 1 | 11 |
| β-strand | 15 | 1 | 17 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-29 | 7 | 17 |
| β-strand | 37-42 | 6 | 17 |
| β-strand | 48-51 | 4 | 17 |
| α-helix | 57-65 | 9 | |
Chain H: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 6 |
| β-strand | 11 | 1 | 5 |
| β-strand | 15 | 1 | 18 |
| α-helix | 20-22 | 3 | |
| β-strand | 23-28 | 6 | 19 |
| β-strand | 38-42 | 5 | 19 |
| β-strand | 48-50 | 3 | 19 |
| β-strand | 51 | 1 | 18 |
| α-helix | 56-63 | 8 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| CXCL12 protein | A, B, C, D, E, F, G, H, I, J | protein | 68 | Homo sapiens | P48061 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA
>3HP3_1 CXCL12 protein (chains A, B, C, D, E, F, G, H, I, J)
MKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQ
EYLEKALN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| AU | Gold ion | Au | 12 |
Primary citation
Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family. Murphy, J.W., Yuan, H., Kong, Y. et al. Proteins (2009) 78:1331-1337. DOI 10.1002/prot.22666 · PubMed
Other PDB entries of the same protein (UniProt P48061 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3GV3 1.6 Å, CXCL12 (SDF) in trigonal space group
- 6SHR 1.75 Å, X-ray crystal structure of cell-free protein synthesis (CFPS) produced SDF1-a
- 4UAI 1.9 Å, Crystal structure of CXCL12 in complex with inhibitor
- 2J7Z 1.95 Å, Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
- 1QG7 2.0 Å, Stroma cell-derived factor-1ALPHA (sdf-1ALPHA)
- 2NWG 2.07 Å, Structure of CXCL12:heparin disaccharide complex
- 1A15 2.2 Å, Sdf-1ALPHA
- 9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
- 4LMQ 2.77 Å, Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12
- 9UPU 2.8 Å, Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
- 8K3Z 2.81 Å, Cryo-EM structure of CXCR4 in complex with CXCL12
- 8U4O 3.29 Å, Structure of CXCL12-bound CXCR4/Gi complex
Browse structure collections
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