Research workbench
Near-atomic resolution cryo-EM structure of the periplasmic domains of prgh and prgk
Analyse Near-atomic resolution cryo-EM structure of the periplasmic domains of prgh and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TCP
- Type
- protein
- Length
- 9,072 residues
- Chains
- 48
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein prgk; Protein prgh
- UniProt
- P41786, P41783
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0, 2, 4, 6, 8, B, D, F, H, J, L, N, P, R, T, V, X, Z, a, c, e, g, i, k | Lipoprotein prgk | protein | 184 | 38% helix, 21% strand | P41786 |
| 1, 3, 5, 7, 9, A, C, E, G, I, K, M, O, Q, S, U, W, Y, b, d, f, h, j, l | Protein prgh | protein | 194 | 42% helix, 26% strand | P41783 |
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 | 1143 | 0.89 | 0.91 | 230 | empty |
| 2 | 1183 | 0.86 | 0.87 | 127 | empty |
| 3 | 961 | 0.86 | 0.87 | 180 | empty |
| 4 | 694 | 0.85 | 0.89 | 95 | empty |
| 5 | 860 | 0.83 | 0.85 | 76 | empty |
Interfaces
96 interfaces between chains.
- a–c · 2426 Ų buried · 25 hydrogen bonds · protein-protein
- R–T · 2420 Ų buried · 25 hydrogen bonds · protein-protein
- 6–8 · 2420 Ų buried · 25 hydrogen bonds · protein-protein
- V–X · 2419 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 2418 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5TCP · Near-atomic resolution cryo-EM structure of the periplasmic domains of PrgH and PrgK · 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 P41786
- Every structure of UniProt P41783
- Elsewhere: RCSB PDB 5TCP · PDBe 5TCP · UniProt P41786 · UniProt P41783
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