MolNFT v1 · #146862 · protein
Structure of the periplasmic domains of prgh and prgk from the assembled salmonella type III secretion injectisome needle complex
6DUZ · Protein prgh: “Structure of the periplasmic domains of prgh and prgk from the assembled salmonella type III secretion…”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #146862 on GenesisL1: 3D structure, binding…
- 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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