MolNFT v1 · #40275 · protein
Crystal structure of nicotinate phosphoribosyltransferase from porphyromonas gingivalis
2IM5: “Crystal structure of nicotinate phosphoribosyltransferase from porphyromonas gingivalis”. X-ray diffraction, 13 pockets (best druggability 0.80). MolNFT v1 #40275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IM5
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate phosphoribosyltransferase
- UniProt
- Q7MXV0
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nicotinate phosphoribosyltransferase | protein | 389 | 50% helix, 16% strand | Q7MXV0 |
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.80 | 0.81 | 122 | empty |
| 2 | 759 | 0.75 | 0.80 | 73 | empty |
| 3 | 452 | 0.75 | 0.84 | 54 | empty |
| 4 | 906 | 0.75 | 0.78 | 79 | empty |
| 5 | 463 | 0.75 | 0.84 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–D · 736 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 725 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 498 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 494 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2IM5 · Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7MXV0
- Elsewhere: RCSB PDB 2IM5 · PDBe 2IM5 · UniProt Q7MXV0
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