MolNFT v1 · #169117 · protein
Tubulin-RB3_SLD-ttl in complex with compound 5J
6X1C · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound 5J”. X-ray diffraction, 6 ligands (GTP, Y5J, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #169117 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6X1C
- Type
- protein
- Length
- 2,174 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, A0A287AGU7, P63043, E1BQ43
- Ligands
- GTP, Y5J, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 427 | 47% helix, 20% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 20% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 78% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 328 | 32% helix, 24% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- Y5J · 4-(2-chlorofuro[3,2-d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.86 | 0.96 | 60 | GTP, MG, Y5J |
| 2 | 1139 | 0.82 | 0.83 | 117 | GDP, MG |
| 3 | 128 | 0.79 | 0.97 | 27 | Y5J |
| 4 | 620 | 0.76 | 0.83 | 71 | GTP, MG |
| 5 | 166 | 0.76 | 0.93 | 29 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1652 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1502 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1401 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 892 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 838 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6X1C · Tubulin-RB3_SLD-TTL in complex with compound 5j · 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 Q2XVP4
- Every structure of UniProt A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6X1C · PDBe 6X1C · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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