MolNFT v1 · #111379 · protein
Crystal structure of methanobacterium thermoautotrophicum nmnat in complex with NADP
4YP5 · Nicotinamide-nucleotide adenylyltransferase: “Crystal structure of methanobacterium thermoautotrophicum nmnat in complex with NADP”. X-ray diffraction, 1 ligand (NAP), 3 pockets (best druggability 0.59). MolNFT v1 #111379 on…
- PDB
- 4YP5
- Type
- protein
- Length
- 505 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide-nucleotide adenylyltransferase
- EC
- 2.7.7.1
- UniProt
- O26253
- Ligands
- NAP
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1) | protein | 167 | 46% helix, 14% strand | O26253 |
| B, C | Nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1) | protein | 169 | 47% helix, 14% strand | O26253 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.59 | 0.76 | 37 | NAP |
| 2 | 308 | 0.58 | 0.77 | 37 | NAP |
| 3 | 267 | 0.53 | 0.76 | 34 | NAP |
Interfaces
3 interfaces between chains.
- A–C · 511 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4YP5 · Crystal structure of Methanobacterium thermoautotrophicum NMNAT in complex with NADP · the same entry in another collection · chain A against A, TM-score 1.00
- O26253 · AlphaFold monomer V2.0 prediction for nicotinamide-nucleotide adenylyltransferase (O26253) · a predicted model of the same protein · chain A 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 O26253
- Elsewhere: RCSB PDB 4YP5 · PDBe 4YP5 · UniProt O26253
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