Research workbench
DELTAC2 C-terminal truncation of HSNMT1 in complex with myrcoa and gncfskpr substrates
Analyse DELTAC2 C-terminal truncation of HSNMT1 in complex with myrcoa and gncfskpr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SKJ
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase 1; Apoptosis-inducing factor 3
- EC
- 2.3.1.97, 1.-.-.-
- UniProt
- P30419, Q96NN9
- Ligands
- MYA, COA, MYR, MG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 387 | 28% helix, 29% strand | P30419 |
| B | Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) | protein | 390 | 28% helix, 28% strand | P30419 |
| C, D | Apoptosis-inducing factor 3 (EC 1.-.-.-) | protein | 8 | 0% helix, 13% strand | Q96NN9 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, C, B, D
- COA · Coenzyme A · ligand · chains B, D
- MYR · Myristic acid · ligand · chains B, D
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.84 | 0.95 | 34 | empty |
| 2 | 200 | 0.82 | 0.96 | 42 | empty |
| 3 | 858 | 0.78 | 0.81 | 83 | empty |
| 4 | 737 | 0.77 | 0.81 | 61 | MYA |
| 5 | 656 | 0.74 | 0.80 | 59 | COA, MYR, MYA |
Interfaces
3 interfaces between chains.
- A–B · 925 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 876 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 785 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 lipid (covalent ligand, myristoylation).
Compared structures
- 6SKJ · DeltaC2 C-terminal truncation of HsNMT1 in complex with MyrCoA and GNCFSKPR substrates · the same entry in another collection · chain D against D, TM-score 1.00
- P30419 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase 1 (P30419) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q96NN9 · AlphaFold monomer V2.0 prediction for apoptosis-inducing factor 3 (Q96NN9) · a predicted model of the same protein · chain C against A, TM-score 0.57
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 P30419
- Every structure of UniProt Q96NN9
- Elsewhere: RCSB PDB 6SKJ · PDBe 6SKJ · UniProt P30419 · UniProt Q96NN9
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