MolNFT v1 · #88756 · protein
Crystal structure of the KTI11 KTI13 heterodimer spacegroup P64
4D4O · Protein ATS1, diphthamide biosynthesis protein 3: “Crystal structure of the KTI11 KTI13 heterodimer spacegroup P64”. X-ray diffraction, 2 ligands (FE, SO4), 8 pockets (best druggability 0.76). MolNFT v1 #88756 on GenesisL1: 3D…
- PDB
- 4D4O
- Type
- protein
- Length
- 820 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ATS1, diphthamide biosynthesis protein 3
- UniProt
- P31386, Q3E840
- Ligands
- FE, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 414 | 6% helix, 45% strand | P31386, Q3E840 |
| B | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 331 | 1% helix, 50% strand | P31386, Q3E840 |
| C | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 75 | 24% helix, 33% strand | P31386, Q3E840 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.76 | 0.81 | 65 | empty |
| 2 | 535 | 0.76 | 0.83 | 49 | empty |
| 3 | 396 | 0.60 | 0.76 | 55 | empty |
| 4 | 305 | 0.59 | 0.78 | 37 | empty |
| 5 | 141 | 0.50 | 0.79 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1182 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 861 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4D4O · Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P64 · the same entry in another collection · chain C against C, TM-score 1.00
- P31386 · AlphaFold monomer V2.0 prediction for protein KTI13 (P31386) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q3E840 · AlphaFold monomer V2.0 prediction for diphthamide biosynthesis protein 3 (Q3E840) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P31386
- Every structure of UniProt Q3E840
- Elsewhere: RCSB PDB 4D4O · PDBe 4D4O · UniProt P31386 · UniProt Q3E840
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