Research workbench
Nap protein from helicobacter pylori
Analyse Nap protein from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JI4
- Type
- protein
- Length
- 1,728 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neutrophil-activating protein a
- UniProt
- P43313
- Ligands
- FE, UNX
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Neutrophil-activating protein a | protein | 144 | 78% helix, 3% strand | P43313 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
- UNX · Unknown atom or ion · ion · 12 copies · chains A, D, G, B, C, E, F, H, K, I, J, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.80 | 0.81 | 101 | UNX, MPD |
| 2 | 1167 | 0.80 | 0.81 | 104 | UNX, MPD, FE |
| 3 | 754 | 0.77 | 0.81 | 66 | MPD, UNX, FE |
| 4 | 747 | 0.77 | 0.81 | 71 | UNX, MPD |
| 5 | 400 | 0.70 | 0.81 | 40 | MPD |
Interfaces
30 interfaces between chains.
- I–L · 1327 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 1321 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1317 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1316 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1315 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1JI4 · NAP protein from helicobacter pylori · the same entry in another collection · chain L against L, 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 P43313
- Elsewhere: RCSB PDB 1JI4 · PDBe 1JI4 · UniProt P43313
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