MolNFT v1 · #99734 · protein
H.INFLUENZAE trmd in complex with N-(4-{[(1H-imidazol-2-ylmethyl) AMINO]METHYL}BENZYL)-4-oxo-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5- carboxamide
4MCB · TRNA (guanine-N(1)-)-methyltransferase: “H.INFLUENZAE trmd in complex with N-(4-{[(1H-imidazol-2-ylmethyl)…”. X-ray diffraction, 2 ligands (21W, SO4), 3 pockets (best druggability 0.75). MolNFT v1 #99734 on GenesisL1: 3D structure…
- PDB
- 4MCB
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- P43912
- Ligands
- 21W, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 205 | 36% helix, 19% strand | P43912 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 243 | 43% helix, 16% strand | P43912 |
Ligands and binding sites
- 21W · N-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.75 | 0.79 | 64 | 21W |
| 2 | 339 | 0.63 | 0.79 | 45 | 21W |
| 3 | 75 | 0.39 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3421 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 4MCB · H.influenzae TrmD in complex with N-(4-{[(1H-IMIDAZOL-2-YLMETHYL)AMINO]METHYL}BENZYL)-4-OX… · the same entry in another collection · chain A against A, TM-score 1.00
- P43912 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P43912) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P43912
- Elsewhere: RCSB PDB 4MCB · PDBe 4MCB · UniProt P43912
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