MolNFT v1 · #61705 · protein
Crystal structure of invasion associated protein B from bartonella henselae
3DTD · Invasion-associated protein B: “Crystal structure of invasion associated protein B from bartonella henselae”. X-ray diffraction, 14 pockets (best druggability 0.73). MolNFT v1 #61705 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DTD
- Type
- protein
- Length
- 1,734 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invasion-associated protein B
- UniProt
- Q6G4Y3
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Invasion-associated protein B | protein | 142 | 15% helix, 50% strand | Q6G4Y3 |
| B | Invasion-associated protein B | protein | 146 | 16% helix, 49% strand | Q6G4Y3 |
| C | Invasion-associated protein B | protein | 147 | 16% helix, 50% strand | Q6G4Y3 |
| D, I, J, K, L | Invasion-associated protein B | protein | 145 | 15% helix, 52% strand | Q6G4Y3 |
| E, G | Invasion-associated protein B | protein | 143 | 15% helix, 51% strand | Q6G4Y3 |
| H | Invasion-associated protein B | protein | 146 | 15% helix, 50% strand | Q6G4Y3 |
Ligands and binding sites
- GOL · Glycerol · additive · 18 copies · chains B, C, G, D, F, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.73 | 0.77 | 74 | empty |
| 2 | 753 | 0.72 | 0.78 | 71 | empty |
| 3 | 626 | 0.70 | 0.78 | 60 | empty |
| 4 | 806 | 0.66 | 0.74 | 104 | empty |
| 5 | 428 | 0.64 | 0.77 | 31 | empty |
Interfaces
21 interfaces between chains.
- K–L · 578 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 578 Ų buried · 11 hydrogen bonds · protein-protein
- B–J · 575 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 571 Ų buried · 9 hydrogen bonds · protein-protein
- H–K · 529 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 3DTD · Crystal structure of invasion associated protein b from bartonella henselae · 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 Q6G4Y3
- Elsewhere: RCSB PDB 3DTD · PDBe 3DTD · UniProt Q6G4Y3
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