Research workbench
Crystal structure of NTMT1 in complex with rpkria peptide
Analyse Crystal structure of NTMT1 in complex with rpkria peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E1O
- Type
- protein
- Length
- 465 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, 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 | 39% helix, 27% strand | Q9BV86 |
| B | N-terminal xaa-pro-lys N-methyltransferase 1 (EC 2.1.1.244) | protein | 226 | 42% 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, B
- UNX · Unknown atom or ion · ion · 36 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, D, 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 | 150 | 0.80 | 0.96 | 29 | SAH |
| 2 | 141 | 0.78 | 0.95 | 29 | SAH |
| 3 | 224 | 0.57 | 0.79 | 36 | GOL |
| 4 | 130 | 0.44 | 0.77 | 27 | UNX |
| 5 | 72 | 0.33 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 554 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 510 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 506 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5E1O · Crystal structure of NTMT1 in complex with RPKRIA peptide · the same entry in another collection · chain D against D, 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 0.98
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 5E1O · PDBe 5E1O · UniProt Q9BV86
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