MolNFT v1 · #66396 · protein
Crystal structure of CXCL12
3HP3 · CXCL12 protein: “Crystal structure of CXCL12”. X-ray diffraction, 1 ligand (AU), 10 pockets (best druggability 0.69). MolNFT v1 #66396 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HP3
- Type
- protein
- Length
- 637 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CXCL12 protein
- UniProt
- Q6ICW0
- Ligands
- AU
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, H | CXCL12 protein | protein | 64 | 17% helix, 27% strand | Q6ICW0 |
| B | CXCL12 protein | protein | 62 | 16% helix, 29% strand | Q6ICW0 |
| E | CXCL12 protein | protein | 61 | 16% helix, 33% strand | Q6ICW0 |
| F, G, I | CXCL12 protein | protein | 65 | 20% helix, 26% strand | Q6ICW0 |
| J | CXCL12 protein | protein | 63 | 17% helix, 29% strand | Q6ICW0 |
Ligands and binding sites
- AU · Gold ion · metal · 12 copies · chains A, B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.69 | 0.84 | 32 | empty |
| 2 | 318 | 0.62 | 0.79 | 40 | empty |
| 3 | 328 | 0.55 | 0.75 | 36 | AU |
| 4 | 57 | 0.55 | 0.88 | 13 | empty |
| 5 | 282 | 0.51 | 0.74 | 37 | AU |
Interfaces
17 interfaces between chains.
- A–B · 1140 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1120 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1043 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 1006 Ų buried · 19 hydrogen bonds · protein-protein
- D–H · 889 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3HP3 · Crystal structure of CXCL12 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6ICW0
- Elsewhere: RCSB PDB 3HP3 · PDBe 3HP3 · UniProt Q6ICW0
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