Research workbench
T=1 capsid structure of semv NDEL65CP fused with B-domain of S. aureus protein spa at the N-terminus (C2 crystal form)
Analyse T=1 capsid structure of semv NDEL65CP fused with B-domain of S. aureus protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y4Y
- Type
- protein
- Length
- 5,730 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein A,COAT protein
- UniProt
- P02976, Q9EB06
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d | Immunoglobulin G-binding protein A,COAT protein | protein | 191 | 20% helix, 41% strand | P02976, Q9EB06 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, H, I, J, Z, a, K, L, b, M, N, c, O, P, Q, S, d, F, G, R, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 737 | 0.88 | 0.92 | 55 | empty |
| 2 | 734 | 0.88 | 0.92 | 54 | empty |
| 3 | 719 | 0.88 | 0.92 | 51 | empty |
| 4 | 724 | 0.88 | 0.92 | 52 | empty |
| 5 | 822 | 0.80 | 0.83 | 123 | empty |
Interfaces
86 interfaces between chains.
- F–G · 1021 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1018 Ų buried · 20 hydrogen bonds · protein-protein
- Z–a · 1018 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1017 Ų buried · 19 hydrogen bonds · protein-protein
- V–W · 1015 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 4Y4Y · T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the… · the same entry in another collection · chain A against A, 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 P02976
- Every structure of UniProt Q9EB06
- Elsewhere: RCSB PDB 4Y4Y · PDBe 4Y4Y · UniProt P02976 · UniProt Q9EB06
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