MolNFT v1 · #165611 · protein
Protofilament ribbon flagellar proteins RIB43A-L
6U0U · Tubulin alpha chain: “Protofilament ribbon flagellar proteins RIB43A-L”. Electron microscopy, 3 ligands (GTP, GDP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #165611 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6U0U
- Type
- protein
- Length
- 5,207 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Protofilament ribbon protein
- UniProt
- P41351, P41352, Q240R7
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F, G, H | Tubulin alpha chain | protein | 429 | 43% helix, 17% strand | P41351 |
| B, I, J, K, L, M | Tubulin beta chain | protein | 420 | 45% helix, 18% strand | P41352 |
| A | Protofilament ribbon protein | protein | 113 | 85% helix, 0% strand | Q240R7 |
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
- MG · Magnesium ion · metal · 6 copies · chains C, B, D, E, J, F, G, H
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 | 238 | 0.83 | 0.95 | 45 | GTP, MG |
| 2 | 217 | 0.82 | 0.95 | 47 | GTP, MG |
| 3 | 233 | 0.82 | 0.95 | 44 | GTP, MG |
| 4 | 205 | 0.82 | 0.96 | 42 | GTP, MG |
| 5 | 764 | 0.82 | 0.85 | 90 | GDP |
Interfaces
25 interfaces between chains.
- C–B · 2004 Ų buried · 16 hydrogen bonds · protein-protein
- E–J · 1965 Ų buried · 16 hydrogen bonds · protein-protein
- H–M · 1961 Ų buried · 22 hydrogen bonds · protein-protein
- G–L · 1936 Ų buried · 15 hydrogen bonds · protein-protein
- C–I · 1931 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6U0U · Protofilament Ribbon Flagellar Proteins Rib43a-L · the same entry in another collection · chain M against M, 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 Q240R7
- Elsewhere: RCSB PDB 6U0U · PDBe 6U0U · UniProt P41351 · UniProt P41352 · UniProt Q240R7
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