Research workbench
Octamer C-domain P140 mycoplasma genitalium.
Analyse Octamer C-domain P140 mycoplasma genitalium. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RCD
- Type
- protein
- Length
- 782 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mgpa adhesin
- UniProt
- D5FY31
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mgpa adhesin | protein | 98 | 16% helix, 37% strand | D5FY31 |
| B | Mgpa adhesin | protein | 96 | 17% helix, 39% strand | D5FY31 |
| C | Mgpa adhesin | protein | 97 | 16% helix, 38% strand | D5FY31 |
| D, E | Mgpa adhesin | protein | 99 | 16% helix, 36% strand | D5FY31 |
| F, X | Mgpa adhesin | protein | 97 | 16% helix, 37% strand | D5FY31 |
| G | Mgpa adhesin | protein | 99 | 17% helix, 37% strand | D5FY31 |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.71 | 0.81 | 55 | empty |
| 2 | 495 | 0.71 | 0.80 | 64 | empty |
| 3 | 431 | 0.70 | 0.81 | 57 | empty |
| 4 | 188 | 0.63 | 0.84 | 18 | empty |
| 5 | 176 | 0.60 | 0.82 | 25 | empty |
Interfaces
23 interfaces between chains.
- B–X · 1361 Ų buried · 19 hydrogen bonds · protein-protein
- C–G · 1349 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1338 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1310 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1300 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6RCD · Octamer C-Domain P140 Mycoplasma genitalium. · 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 D5FY31
- Elsewhere: RCSB PDB 6RCD · PDBe 6RCD · UniProt D5FY31
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.