MolNFT v1 · #41843 · protein
Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines
2K04 · Stromal cell-derived factor 1: “Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines”. Solution nmr, 4 pockets (best druggability 0.43). MolNFT v1 #41843 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2K04
- 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
- 4 · best druggability 0.43
Structure
solution nmr · 2 distinct chains · 12% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Stromal cell-derived factor 1 | protein | 68 | 19% helix, 24% strand | P48061 |
| B, D | C-X-C chemokine receptor type 4 | protein | 38 | 0% helix, 0% strand | P61073 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.43 | 0.82 | 15 | empty |
| 2 | 124 | 0.40 | 0.75 | 23 | empty |
| 3 | 56 | 0.39 | 0.80 | 19 | empty |
| 4 | 100 | 0.37 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1293 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1238 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 879 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 655 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2K04 · Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines · 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 0.79
- 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 0.27
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 2K04 · PDBe 2K04 · UniProt P48061 · UniProt P61073
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