MolNFT v1 · #67517 · protein
New crystal form of the C-terminal domain of helicobacter pylori motb (residues 125-256)
3IMP · Chemotaxis protein motb: “New crystal form of the C-terminal domain of helicobacter pylori motb (residues 125-256)”. X-ray diffraction, 2 ligands (NI, CL), 20 pockets (best druggability 0.81). MolNFT v1 #67517 on GenesisL1: 3D…
- PDB
- 3IMP
- Type
- protein
- Length
- 1,586 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemotaxis protein motb
- UniProt
- P56427
- Ligands
- NI, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, F | Chemotaxis protein motb | protein | 133 | 44% helix, 16% strand | P56427 |
| D, E, G, H, I, J, K, L | Chemotaxis protein motb | protein | 132 | 45% helix, 17% strand | P56427 |
| A | Chemotaxis protein motb | protein | 131 | 43% helix, 17% strand | P56427 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains G, K
- CL · Chloride ion · ion · 4 copies · chains G, E, C, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.81 | 0.83 | 96 | empty |
| 2 | 345 | 0.74 | 0.86 | 52 | NI, CL |
| 3 | 183 | 0.67 | 0.86 | 41 | empty |
| 4 | 186 | 0.67 | 0.86 | 28 | CL |
| 5 | 155 | 0.61 | 0.85 | 35 | empty |
Interfaces
29 interfaces between chains.
- F–G · 913 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 871 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 865 Ų buried · 13 hydrogen bonds · protein-protein
- J–K · 858 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 844 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3IMP · New crystal form of the C-terminal domain of Helicobacter pylori MotB (residues 125-256) · 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 P56427
- Elsewhere: RCSB PDB 3IMP · PDBe 3IMP · UniProt P56427
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