MolNFT v1 · #120648 · protein
Crystal structure of T2R-ttl-14B complex
5H74 · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-14B complex”. X-ray diffraction, 6 ligands (GTP, 7LG, GDP), 20 pockets (best druggability 0.82). MolNFT v1 #120648 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H74
- Type
- protein
- Length
- 2,184 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; Uncharacterized protein
- UniProt
- Q2XVP4, Q6B856, P63043, E1BQ43
- Ligands
- GTP, 7LG, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 428 | 48% helix, 18% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 424 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 75% helix, 13% strand | P63043 |
| F | Uncharacterized protein | protein | 334 | 30% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- 7LG · (2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[hexyl-[(2~{S},3~{S})-3-methyl-2-[[(2~{R})-1-methylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-4-methyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-fluorophenyl)-2-methyl-pentanoic acid · ligand · 2 copies · chains B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.82 | 0.83 | 108 | GDP, MG, 7LG |
| 2 | 1025 | 0.80 | 0.82 | 105 | GTP, MG |
| 3 | 1168 | 0.80 | 0.82 | 128 | GTP, MG |
| 4 | 138 | 0.77 | 0.95 | 34 | empty |
| 5 | 74 | 0.73 | 0.97 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1656 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1452 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1430 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 914 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 831 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5H74 · Crystal structure of T2R-TTL-14b complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q6B856 · AlphaFold monomer V2.0 prediction for tubulin beta-2B chain (Q6B856) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P63043 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63043) · a predicted model of the same protein · chain E against A, TM-score 0.77
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 Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5H74 · PDBe 5H74 · UniProt Q2XVP4 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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