Research workbench
Protofilament ribbon flagellar proteins RIB43A-S
Analyse Protofilament ribbon flagellar proteins RIB43A-S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U0T
- Type
- protein
- Length
- 5,230 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; RIB43A protein
- UniProt
- P41351, P41352, A4VDZ5
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F, G, H | Tubulin alpha chain | protein | 429 | 42% helix, 16% strand | P41351 |
| B, I, J, K, L, M | Tubulin beta chain | protein | 420 | 45% helix, 18% strand | P41352 |
| A | RIB43A protein | protein | 136 | 76% helix, 1% strand | A4VDZ5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains C, B, D, I, E, J, F, K, G, L, H, M
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains B, C, I, J, K, F, L, G, M, A
- MG · Magnesium ion · metal · 6 copies · chains C, B, D, E, F, G, H, M
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 | 372 | 0.85 | 0.94 | 58 | GDP |
| 2 | 266 | 0.84 | 0.95 | 47 | GTP, MG |
| 3 | 255 | 0.83 | 0.95 | 47 | GTP, MG |
| 4 | 231 | 0.83 | 0.95 | 46 | GTP, MG |
| 5 | 249 | 0.82 | 0.95 | 46 | GTP, MG |
Interfaces
25 interfaces between chains.
- C–B · 1999 Ų buried · 12 hydrogen bonds · protein-protein
- C–I · 1961 Ų buried · 23 hydrogen bonds · protein-protein
- E–J · 1955 Ų buried · 16 hydrogen bonds · protein-protein
- D–I · 1915 Ų buried · 21 hydrogen bonds · protein-protein
- G–L · 1909 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6U0T · Protofilament Ribbon Flagellar Proteins Rib43a-S · 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 P41351
- Every structure of UniProt P41352
- Every structure of UniProt A4VDZ5
- Elsewhere: RCSB PDB 6U0T · PDBe 6U0T · UniProt P41351 · UniProt P41352 · UniProt A4VDZ5
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