MolNFT v1 · #97524 · protein
Crystal structure of a tRNA (CYTIDINE(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine
4KGN: “Crystal structure of a tRNA (CYTIDINE(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine”. X-ray diffraction, 2 ligands (SAH, CL), 16 pockets (best druggability 0.72). MolNFT v1 #97524 on GenesisL1: 3D structure, binding…
- PDB
- 4KGN
- Type
- protein
- Length
- 1,220 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CYTIDINE(34)-2'-O)-methyltransferase
- EC
- 2.1.1.207
- UniProt
- Q3JWH1
- Ligands
- SAH, CL
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 139 | 34% helix, 21% strand | Q3JWH1 |
| B, E, H | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 156 | 38% helix, 19% strand | Q3JWH1 |
| C | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 157 | 38% helix, 17% strand | Q3JWH1 |
| D | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 150 | 37% helix, 19% strand | Q3JWH1 |
| F | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 158 | 38% helix, 18% strand | Q3JWH1 |
| G | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 148 | 36% helix, 19% strand | Q3JWH1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, E, C, G
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.72 | 0.76 | 110 | SAH, CL |
| 2 | 709 | 0.71 | 0.78 | 72 | SAH, CL |
| 3 | 401 | 0.66 | 0.79 | 50 | empty |
| 4 | 310 | 0.63 | 0.80 | 43 | SAH |
| 5 | 238 | 0.61 | 0.81 | 29 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1592 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1586 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1558 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 396 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4KGN · Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl… · the same entry in another collection · chain B against B, 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 Q3JWH1
- Elsewhere: RCSB PDB 4KGN · PDBe 4KGN · UniProt Q3JWH1
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