Research workbench
Structural and functional studies of the potent anti-HIV chemokine variant P2-rantes
Analyse Structural and functional studies of the potent anti-HIV chemokine variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VXW
- Type
- protein
- Length
- 263 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C motif chemokine 5
- UniProt
- P13501
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-C motif chemokine 5 | protein | 69 | 20% helix, 33% strand | P13501 |
| C | C-C motif chemokine 5 | protein | 63 | 24% helix, 29% strand | P13501 |
| D | C-C motif chemokine 5 | protein | 62 | 16% helix, 29% strand | P13501 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.45 | 0.77 | 23 | empty |
| 2 | 56 | 0.43 | 0.82 | 21 | empty |
| 3 | 51 | 0.42 | 0.83 | 17 | empty |
| 4 | 67 | 0.36 | 0.77 | 22 | empty |
| 5 | 63 | 0.30 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 761 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 463 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VXW · Structural and Functional Studies of the Potent Anti-HIV Chemokine Variant P2-RANTES · the same entry in another collection · chain D against D, TM-score 1.00
- P13501 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 5 (P13501) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P13501
- Elsewhere: RCSB PDB 2VXW · PDBe 2VXW · UniProt P13501
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