Research workbench
Crystal structure of the KTI11 KTI13 heterodimer spacegroup P65
Analyse Crystal structure of the KTI11 KTI13 heterodimer spacegroup P65 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D4P
- Type
- protein
- Length
- 1,642 residues
- Chains
- 6
- 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
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 413 | 5% helix, 45% strand | P31386, Q3E840 |
| B | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 336 | 1% helix, 49% strand | P31386, Q3E840 |
| C | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 76 | 24% helix, 34% strand | P31386, Q3E840 |
| E | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 334 | 1% helix, 49% strand | P31386, Q3E840 |
| G | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 409 | 6% helix, 44% strand | P31386, Q3E840 |
| H | Protein ATS1, diphthamide biosynthesis protein 3 | protein | 74 | 16% helix, 35% strand | P31386, Q3E840 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, C, G, H
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.80 | 0.86 | 91 | empty |
| 2 | 761 | 0.78 | 0.82 | 78 | empty |
| 3 | 342 | 0.77 | 0.88 | 58 | empty |
| 4 | 715 | 0.77 | 0.81 | 63 | empty |
| 5 | 533 | 0.76 | 0.83 | 47 | empty |
Interfaces
9 interfaces between chains.
- E–G · 1204 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1173 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 867 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 847 Ų buried · 18 hydrogen bonds · protein-protein
- A–G · 637 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4D4P · Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P65 · 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 E 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 H against A, TM-score 0.92
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 4D4P · PDBe 4D4P · UniProt P31386 · UniProt Q3E840
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