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Crystal structure of 8-mer peptide from rous sarcoma virus in complex with BF2*1201
Analyse Crystal structure of 8-mer peptide from rous sarcoma virus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YMW
- Type
- protein
- Length
- 1,508 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class I histocompatibility antigen, F10 alpha chain; Beta-2-microglobulin…
- UniProt
- P15979, P21611
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Class I histocompatibility antigen, F10 alpha chain | protein | 271 | 28% helix, 43% strand | P15979 |
| B, E, H, K | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P21611 |
| C, F, I, L | Leu-pro-ala-cys-val-leu-glu-val | protein | 8 | 0% helix, 0% strand | — |
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.80 | 0.82 | 101 | empty |
| 2 | 656 | 0.71 | 0.79 | 51 | empty |
| 3 | 401 | 0.70 | 0.82 | 47 | empty |
| 4 | 485 | 0.67 | 0.78 | 51 | empty |
| 5 | 260 | 0.56 | 0.77 | 32 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1620 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1597 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1592 Ų buried · 26 hydrogen bonds · protein-protein
- J–K · 1563 Ų buried · 27 hydrogen bonds · protein-protein
- A–G · 940 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5YMW · Crystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201 · the same entry in another collection · chain L against L, 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 P15979
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 5YMW · PDBe 5YMW · UniProt P15979 · UniProt P21611
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