Research workbench
Model of the prgh-prgk periplasmic rings
Analyse Model of the prgh-prgk periplasmic rings in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J6D
- Type
- protein
- Length
- 8,136 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein prgh; Pathogenicity 1 island effector protein
- UniProt
- P41783, A0A078PCJ3
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 34% helix, 16% 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 | Protein prgh | protein | 191 | 36% helix, 18% strand | P41783 |
| a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, Y, Z | Pathogenicity 1 island effector protein | protein | 148 | 32% helix, 14% strand | A0A078PCJ3 |
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 | 1200 | 0.79 | 0.80 | 85 | empty |
| 2 | 519 | 0.74 | 0.82 | 55 | empty |
| 3 | 610 | 0.74 | 0.81 | 64 | empty |
| 4 | 692 | 0.74 | 0.80 | 67 | empty |
| 5 | 574 | 0.73 | 0.81 | 50 | empty |
Interfaces
72 interfaces between chains.
- v–Y · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- o–p · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- l–m · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- f–g · 1494 Ų buried · 16 hydrogen bonds · protein-protein
- n–o · 1493 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3J6D · Model of the PrgH-PrgK periplasmic rings · 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 P41783
- Every structure of UniProt A0A078PCJ3
- Elsewhere: RCSB PDB 3J6D · PDBe 3J6D · UniProt P41783 · UniProt A0A078PCJ3
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