Research workbench
Agrobacterium tumefaciens Tpilus
Analyse Agrobacterium tumefaciens Tpilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8EXH
- Type
- protein
- Length
- 2,760 residues
- Chains
- 40
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Agrobacterium fabrum (strain C58 / ATCC 33970)
- Molecule
- Protein virB2
- UniProt
- P17792
- Ligands
- X3D
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.5 · 1 distinct chain · 80% helix, 0% 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, e, f, g, h, i, j, k, l, m, n | Protein virB2 | protein | 69 | 80% helix, 0% strand | P17792 |
Ligands and binding sites
- X3D · (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate · ligand · 40 copies · chains A, E, F, j, k, B, M, m, C, D, J, K, n, L, N, G, O, H, P, Q, I, R, S, T, U, X, V, W, Y, Z, a, b, c, d, e, f, i, g, h, l
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.87 | 0.90 | 61 | X3D |
| 2 | 610 | 0.86 | 0.90 | 60 | X3D |
| 3 | 472 | 0.86 | 0.92 | 67 | X3D |
| 4 | 580 | 0.86 | 0.90 | 55 | X3D |
| 5 | 433 | 0.85 | 0.92 | 56 | X3D |
Interfaces
140 interfaces between chains.
- R–S · 982 Ų buried · 1 hydrogen bond · protein-protein
- C–n · 979 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 976 Ų buried · 1 hydrogen bond · protein-protein
- b–c · 976 Ų buried · 1 hydrogen bond · protein-protein
- Y–Z · 975 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P17792 · AlphaFold monomer V2.0 prediction for protein VIRB2 (P17792) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P17792
- Elsewhere: RCSB PDB 8EXH · PDBe 8EXH · UniProt P17792
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