MolNFT v1 · #41842 · protein
Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21
2K03 · Stromal cell-derived factor 1: “Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21”. Solution nmr, 2 pockets (best druggability 0.47). MolNFT v1 #41842 on GenesisL1: 3D structure…
- PDB
- 2K03
- 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
- 2 · best druggability 0.47
Structure
solution nmr · 2 distinct chains · 13% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Stromal cell-derived factor 1 | protein | 68 | 21% helix, 26% strand | P48061 |
| B, D | C-X-C chemokine receptor type 4 | protein | 38 | 0% helix, 3% strand | P61073 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.47 | 0.81 | 24 | empty |
| 2 | 59 | 0.27 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1376 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1374 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 810 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, sulfation).
Compared structures
- 2K03 · Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine 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 0.78
- P61073 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 4 (P61073) · a predicted model of the same protein · chain B against A, TM-score 0.26
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 2K03 · PDBe 2K03 · UniProt P48061 · UniProt P61073
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