Research workbench
Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21
Analyse Structure of SDF1 in complex with the CXCR4 N-terminus containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2K05
- Type
- protein
- Length
- 212 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stromal cell-derived factor 1; C-X-C chemokine receptor type 4
- UniProt
- P48061, P61073
- Pockets
- 3 · best druggability 0.52
Structure
solution nmr · 2 distinct chains · 9% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Stromal cell-derived factor 1 | protein | 68 | 15% helix, 26% strand | P48061 |
| B, D | C-X-C chemokine receptor type 4 | protein | 38 | 0% helix, 0% strand | P61073 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.52 | 0.88 | 17 | empty |
| 2 | 98 | 0.36 | 0.74 | 20 | empty |
| 3 | 72 | 0.31 | 0.74 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1505 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1368 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 981 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 620 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 601 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, sulfation).
Compared structures
- 2K05 · Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at… · the same entry in another collection · chain A against A, TM-score 1.00
- P48061 · AlphaFold monomer V2.0 prediction for stromal cell-derived factor 1 (P48061) · a predicted model of the same protein · chain A against A, TM-score 0.76
- P61073 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 4 (P61073) · a predicted model of the same protein · chain D against A, TM-score 0.34
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 P48061
- Every structure of UniProt P61073
- Elsewhere: RCSB PDB 2K05 · PDBe 2K05 · UniProt P48061 · UniProt P61073
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