MolNFT v1 · #144843 · protein
20MER crystal structure of cc chemokine 5 (CCL5)
6C6D · C-C motif chemokine 5: “20MER crystal structure of cc chemokine 5 (CCL5)”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #144843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C6D
- Type
- protein
- Length
- 1,264 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C motif chemokine 5
- UniProt
- P13501
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, S, M, O, Q | C-C motif chemokine 5 | protein | 64 | 22% helix, 28% strand | P13501 |
| B, F, H, T, N, R | C-C motif chemokine 5 | protein | 62 | 23% helix, 29% strand | P13501 |
| D, J, P | C-C motif chemokine 5 | protein | 63 | 22% helix, 29% strand | P13501 |
| L | C-C motif chemokine 5 | protein | 63 | 17% helix, 29% strand | P13501 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.76 | 0.97 | 23 | empty |
| 2 | 72 | 0.70 | 0.95 | 15 | empty |
| 3 | 297 | 0.65 | 0.81 | 49 | empty |
| 4 | 341 | 0.64 | 0.79 | 42 | empty |
| 5 | 303 | 0.63 | 0.80 | 45 | empty |
Interfaces
37 interfaces between chains.
- K–L · 778 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 745 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 705 Ų buried · 10 hydrogen bonds · protein-protein
- P–R · 704 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 701 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 6C6D · 20mer crystal structure of CC chemokine 5 (CCL5) · the same entry in another collection · chain K against K, 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 P13501
- Elsewhere: RCSB PDB 6C6D · PDBe 6C6D · UniProt P13501
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