MolNFT v1 · #190196 · protein
Crystal structure of macrocyclic peptide 1 bound to human nicotinamide N-methyltransferase
7WMC: “Crystal structure of macrocyclic peptide 1 bound to human nicotinamide N-methyltransferase”. X-ray diffraction, 2 pockets (best druggability 0.60). MolNFT v1 #190196 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WMC
- Type
- protein
- Length
- 485 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide N-methyltransferase; PEPTIDE1
- EC
- 2.1.1.1
- UniProt
- P40261
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 228 | 43% helix, 26% strand | P40261 |
| C, E, D | PEPTIDE1 | protein | 9 | 0% helix, 0% strand | — |
| B | Nicotinamide N-methyltransferase (EC 2.1.1.1) | protein | 230 | 40% helix, 26% strand | P40261 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.60 | 0.81 | 31 | empty |
| 2 | 195 | 0.54 | 0.78 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1745 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 944 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 912 Ų buried · 14 hydrogen bonds · protein-protein
- E–B · 501 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 419 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7WMC · Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase · the same entry in another collection · chain B against B, TM-score 1.00
- P40261 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (P40261) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P40261
- Elsewhere: RCSB PDB 7WMC · PDBe 7WMC · UniProt P40261
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