Research workbench
Crystal structure of a human rhinovirus type 14:HUMAN immunodeficiency virus type 1 V3 loop chimeric virus mn-III-2
Analyse Crystal structure of a human rhinovirus type 14:HUMAN immunodeficiency virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K5M
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein VP1 (P1D); Chimera of HRV14 coat protein VP2 (P1B) and the V3 loop of HIV-1…
- UniProt
- P03303, P05877
- Ligands
- SPH
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein VP1 (P1D) | protein | 283 | 11% helix, 34% strand | P03303 |
| B | Chimera of HRV14 coat protein VP2 (P1B) and the V3 loop of HIV-1 GP120 | protein | 270 | 15% helix, 35% strand | P03303, P05877 |
| C | Coat protein VP3 (P1C) | protein | 236 | 9% helix, 31% strand | P03303 |
| D | Coat protein VP4 (P1A) | protein | 40 | 18% helix, 3% strand | P03303 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.79 | 0.85 | 67 | SPH |
| 2 | 237 | 0.58 | 0.79 | 33 | empty |
| 3 | 120 | 0.45 | 0.78 | 26 | empty |
| 4 | 100 | 0.45 | 0.79 | 19 | empty |
| 5 | 58 | 0.44 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4166 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 2001 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1800 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 956 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 830 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1K5M · Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3… · the same entry in another collection · chain C against C, 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 P03303
- Every structure of UniProt P05877
- Elsewhere: RCSB PDB 1K5M · PDBe 1K5M · UniProt P03303 · UniProt P05877
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.