Research workbench
Crystal structure of NTMT1 in complex with N-terminally methylated spkria peptide
Analyse Crystal structure of NTMT1 in complex with N-terminally methylated spkria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E2A
- 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
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% 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 | 40% helix, 27% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 225 | 41% helix, 26% 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 · 33 copies · chains A, B, D, E
- GOL · Glycerol · additive · 4 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.80 | 0.96 | 30 | SAH |
| 2 | 143 | 0.79 | 0.96 | 29 | SAH |
| 3 | 306 | 0.67 | 0.82 | 39 | UNX, GOL |
| 4 | 80 | 0.48 | 0.83 | 25 | GOL |
| 5 | 135 | 0.46 | 0.77 | 31 | UNX |
Interfaces
4 interfaces between chains.
- A–D · 529 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 512 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 508 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5E2A · Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA 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 5E2A · PDBe 5E2A · UniProt Q9BV86
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