MolNFT v1 · #117244 · protein
Crystal structure of NTMT1 in complex with N-terminally methylated ppkria peptide
5E2B · N-terminal xaa-pro-lys N-methyltransferase 1: “Crystal structure of NTMT1 in complex with N-terminally methylated ppkria peptide”. X-ray diffraction, 2 ligands (SAH, UNX), 5 pockets (best druggability 0.80). MolNFT v1 #117244 on…
- PDB
- 5E2B
- Type
- protein
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal xaa-pro-lys N-methyltransferase 1; RCC1
- EC
- 2.1.1.244
- UniProt
- Q9BV86
- Ligands
- SAH, UNX
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 227 | 39% helix, 27% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 225 | 41% helix, 27% strand | Q9BV86 |
| D, E | RCC1 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D, B, E
- UNX · Unknown atom or ion · ion · 50 copies · chains A, B, E, D
- GOL · Glycerol · additive · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.96 | 27 | SAH |
| 2 | 144 | 0.78 | 0.95 | 30 | SAH |
| 3 | 279 | 0.65 | 0.82 | 38 | GOL, UNX |
| 4 | 142 | 0.46 | 0.77 | 24 | UNX |
| 5 | 66 | 0.31 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 525 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 488 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5E2B · Crystal structure of NTMT1 in complex with N-terminally methylated PPKRIA peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BV86 · AlphaFold monomer V2.0 prediction for N-terminal xaa-pro-lys N-methyltransferase 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9BV86
- Elsewhere: RCSB PDB 5E2B · PDBe 5E2B · UniProt Q9BV86
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