MolNFT v1 · #170346 · protein
Structure of tubulin tyrosine ligase in complex with TB111
6Y4M: “Structure of tubulin tyrosine ligase in complex with TB111”. X-ray diffraction, 8 ligands (GTP, GDP, O9B). MolNFT v1 #170346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Y4M
- Type
- protein
- Length
- 2,207 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q2XVP4, P02554, P63043, E1BQ43
- Ligands
- GTP, GDP, O9B, O9H, OH5, ACP, MG, CA
Structure
x-ray diffraction · 6 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 439 | — | Q2XVP4 |
| B | — | protein | 431 | — | P02554 |
| C | — | protein | 441 | — | Q2XVP4 |
| D | — | protein | 427 | — | P02554 |
| E | — | protein | 123 | — | P63043 |
| F | — | protein | 346 | — | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- O9B · (2~{R})-1-methylpiperidine-2-carboxylic acid · ligand · chains B, C
- O9H · [(1~{R},3~{R})-1-acetyloxy-1-[4-methanoyl-5-(2-phenylmethoxyethyl)-2,3-dihydro-1,3-thiazol-2-yl]-4-methyl-pentan-3-yl]-methyl-azanium · ligand · chains B, C
- OH5 · (2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid · 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 · chains B
- PGE · Triethylene glycol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6Y4M · Structure of Tubulin Tyrosine Ligase in Complex with Tb111 · the same entry in another collection · chain D against D, 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 P02554
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6Y4M · PDBe 6Y4M · UniProt Q2XVP4 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43
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