MolNFT v1 · #138256 · protein
Structure of the pulg pseudopilus
5WDA · General secretion pathway protein G: “Structure of the pulg pseudopilus”. Electron microscopy, 1 ligand (CA), 20 pockets (best druggability 0.92). MolNFT v1 #138256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WDA
- Type
- protein
- Length
- 3,250 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General secretion pathway protein G
- UniProt
- A0A0G3SCW3
- Ligands
- CA
- Pockets
- 20 · best druggability 0.92
Structure
electron microscopy · 1 distinct chain · 35% helix, 6% 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 | General secretion pathway protein G | protein | 130 | 35% helix, 6% strand | A0A0G3SCW3 |
Ligands and binding sites
- CA · Calcium ion · metal · 25 copies · chains 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1171 | 0.92 | 0.95 | 233 | empty |
| 2 | 949 | 0.92 | 0.95 | 186 | empty |
| 3 | 842 | 0.91 | 0.95 | 170 | empty |
| 4 | 382 | 0.82 | 0.90 | 66 | empty |
| 5 | 585 | 0.71 | 0.79 | 62 | empty |
Interfaces
127 interfaces between chains.
- B–E · 766 Ų buried · 1 hydrogen bond · protein-protein
- I–L · 765 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 765 Ų buried · 1 hydrogen bond · protein-protein
- P–S · 764 Ų buried · 1 hydrogen bond · protein-protein
- H–K · 764 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 25 disulfide, 25 modified (disulfide, nonstandard).
Compared structures
- 5WDA · Structure of the PulG pseudopilus · the same entry in another collection · chain B against B, 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 A0A0G3SCW3
- Elsewhere: RCSB PDB 5WDA · PDBe 5WDA · UniProt A0A0G3SCW3
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