MolNFT v1 · #99195 · protein
Crystal structure of vibrio cholera major pseudopilin epsg
4LW9 · Type II secretion system protein G: “Crystal structure of vibrio cholera major pseudopilin epsg”. X-ray diffraction, 6 ligands (ZN, CA, PT), 19 pockets (best druggability 0.77). MolNFT v1 #99195 on GenesisL1: 3D structure, binding…
- PDB
- 4LW9
- Type
- protein
- Length
- 1,414 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein G
- UniProt
- P45773
- Ligands
- ZN, CA, PT, NA, SO4, CL
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, J, Q | Type II secretion system protein G | protein | 119 | 38% helix, 9% strand | P45773 |
| B, C, E, L, R | Type II secretion system protein G | protein | 118 | 37% helix, 9% strand | P45773 |
| F | Type II secretion system protein G | protein | 114 | 35% helix, 10% strand | P45773 |
| I | Type II secretion system protein G | protein | 117 | 34% helix, 9% strand | P45773 |
| K | Type II secretion system protein G | protein | 117 | 35% helix, 9% strand | P45773 |
Ligands and binding sites
- ZN · Zinc ion · metal · 32 copies · chains A, B, C, D, R, E, F, I, J, K, L, Q
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D, E, F, I, J, K, L, Q, R
- PT · Platinum (II) ion · metal · 12 copies · chains A, B, C, D, E, F, I, J, K, L, Q, R
- NA · Sodium ion · metal · 6 copies · chains A, B, I, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D, E, F, I, J, K, L, Q, R
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D, E, F, K, L, R, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.77 | 0.86 | 52 | PT, CL, SO4 |
| 2 | 383 | 0.77 | 0.86 | 46 | PT, SO4 |
| 3 | 664 | 0.75 | 0.81 | 50 | PT, CL |
| 4 | 884 | 0.74 | 0.78 | 75 | CL, PT |
| 5 | 714 | 0.68 | 0.76 | 59 | SO4 |
Interfaces
17 interfaces between chains.
- A–B · 851 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 831 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 824 Ų buried · 16 hydrogen bonds · protein-protein
- Q–R · 800 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 754 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4LW9 · Crystal structure of Vibrio cholera major pseudopilin EpsG · the same entry in another collection · chain R against R, 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 P45773
- Elsewhere: RCSB PDB 4LW9 · PDBe 4LW9 · UniProt P45773
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