MolNFT v1 · #128086 · protein
Tubulin-mtc-zampanolide complex
5NG1 · Tubulin alpha-1B chain: “Tubulin-mtc-zampanolide complex”. X-ray diffraction, 8 ligands (GTP, GDP, 8WB), 20 pockets (best druggability 0.86). MolNFT v1 #128086 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NG1
- Type
- protein
- Length
- 2,207 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
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 8WB, 8WE, ZPN, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 420 | 49% helix, 20% strand | Q6B856 |
| D | Tubulin beta-2B chain | protein | 431 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 353 | 32% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- 8WB · 2-methoxy-5-(2,3,4-trimethoxyphenyl)cyclohepta-2,4,6-trien-1-one · ligand · 2 copies · chains A, B, C, D
- 8WE · (2~{Z},4~{E})-~{N}-[(~{S})-oxidanyl-[(1~{S},2~{E}, 5~{S},11~{R},17~{S},19~{R})-3,11,19-trimethyl-7,13-bis(oxidanylidene)-6,21-dioxabicyclo[15.3.1]henicos-2-en-5-yl]methyl]hexa-2,4-dienamide · ligand · chains B
- ZPN · (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide · ligand · chains D
- 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
- GOL · Glycerol · additive · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.86 | 0.95 | 66 | GTP, MG, 8WB |
| 2 | 978 | 0.85 | 0.86 | 128 | GDP, MG, GOL |
| 3 | 315 | 0.84 | 0.94 | 46 | empty |
| 4 | 324 | 0.84 | 0.94 | 58 | GTP, MG, 8WB |
| 5 | 382 | 0.77 | 0.87 | 45 | ACP, MG |
Interfaces
9 interfaces between chains.
- A–E · 1621 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1442 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1397 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 978 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 919 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5NG1 · TUBULIN-MTC-zampanolide complex · 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5NG1 · PDBe 5NG1 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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