Research workbench
Structure of the periplasmic domains of prgh and prgk from the assembled salmonella type III secretion injectisome needle complex
Analyse Structure of the periplasmic domains of prgh and prgk from the assembled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DUZ
- Type
- protein
- Length
- 9,072 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein prgh; Lipoprotein prgk
- UniProt
- P41783, P41786
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 34% helix, 21% 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 | 194 | 36% helix, 22% strand | P41783 |
| Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v | Lipoprotein prgk | protein | 184 | 31% helix, 21% strand | P41786 |
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 | 963 | 0.84 | 0.85 | 88 | empty |
| 2 | 846 | 0.84 | 0.86 | 75 | empty |
| 3 | 880 | 0.83 | 0.86 | 77 | empty |
| 4 | 802 | 0.83 | 0.86 | 74 | empty |
| 5 | 849 | 0.83 | 0.86 | 78 | empty |
Interfaces
120 interfaces between chains.
- d–e · 2603 Ų buried · 29 hydrogen bonds · protein-protein
- p–q · 2587 Ų buried · 25 hydrogen bonds · protein-protein
- m–n · 2569 Ų buried · 26 hydrogen bonds · protein-protein
- Y–v · 2566 Ų buried · 25 hydrogen bonds · protein-protein
- k–l · 2563 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6DUZ · Structure of the periplasmic domains of PrgH and PrgK from the assembled Salmonella type… · the same entry in another collection · chain h against h, 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 P41786
- Elsewhere: RCSB PDB 6DUZ · PDBe 6DUZ · UniProt P41783 · UniProt P41786
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