Research workbench
T=1 capsid structure of semv NDEL65CP fused with B-domain of S. aureus protein spa at the N-terminus (P1 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
- 4Y5Z
- Type
- protein
- Length
- 11,534 residues
- Chains
- 60
- 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 · 6 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, I, K, L, N, O, P, Q, T, U, V, W, Y, Z, a, e, g, i, r, t, u, v, w, x, z, 0, 2, 4, 5, 6, 7, b, h, n, p | Immunoglobulin G-binding protein A,COAT protein | protein | 192 | 20% helix, 39% strand | P02976, Q9EB06 |
| B, X, 3, j | Immunoglobulin G-binding protein A,COAT protein | protein | 194 | 20% helix, 39% strand | P02976, Q9EB06 |
| E, R, S, c | Immunoglobulin G-binding protein A,COAT protein | protein | 191 | 20% helix, 39% strand | P02976, Q9EB06 |
| H, M, k, m, q, s, y, d, f | Immunoglobulin G-binding protein A,COAT protein | protein | 193 | 21% helix, 39% strand | P02976, Q9EB06 |
| J | Immunoglobulin G-binding protein A,COAT protein | protein | 193 | 20% helix, 39% strand | P02976, Q9EB06 |
| o, 1, l | Immunoglobulin G-binding protein A,COAT protein | protein | 192 | 20% helix, 40% strand | P02976, Q9EB06 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains 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, c, e, g, i, k, m, o, q, r, s, t, u, v, w, x, y, z, 0, 1, 2, 3, 4, 5, 6, 7, b, d, f, h, j, l, n, p
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 | 738 | 0.88 | 0.92 | 50 | empty |
| 2 | 694 | 0.88 | 0.93 | 46 | empty |
| 3 | 698 | 0.88 | 0.93 | 49 | empty |
| 4 | 731 | 0.88 | 0.92 | 53 | empty |
| 5 | 732 | 0.88 | 0.92 | 50 | empty |
Interfaces
210 interfaces between chains.
- Q–R · 1062 Ų buried · 20 hydrogen bonds · protein-protein
- o–q · 1061 Ų buried · 21 hydrogen bonds · protein-protein
- R–S · 1060 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1059 Ų buried · 24 hydrogen bonds · protein-protein
- P–Q · 1058 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide (disulfide).
Compared structures
- 4Y5Z · 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 J against J, 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 4Y5Z · PDBe 4Y5Z · UniProt P02976 · UniProt Q9EB06
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