MolNFT v1 · #123702 · protein
Crystal structure of PHIAB6 tailspike in complex with three-repeated oligosaccharides of acinetobacter baumannii surface polysaccharide
5JSE: “Crystal structure of PHIAB6 tailspike in complex with three-repeated oligosaccharides of acinetobacter…”. X-ray diffraction, 4 ligands (1GN, 6PZ, GAL), 10 pockets (best druggability 0.90). MolNFT v1 #123702 on GenesisL1: 3D…
- PDB
- 5JSE
- Type
- protein
- Length
- 1,644 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHIAB6 tailspike
- Ligands
- 1GN, 6PZ, GAL, BGC
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | PHIAB6 tailspike | protein | 548 | 6% helix, 49% strand | — |
Ligands and binding sites
- 1GN · 2-amino-2-deoxy-beta-D-galactopyranose · ligand · 6 copies · chains A, B, C
- 6PZ · 5,7-bisacetamido-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 3 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, B, C
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- MLA · Malonic acid · additive · 6 copies · chains A, B, C
- ACY · Acetic acid · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.90 | 0.92 | 120 | empty |
| 2 | 258 | 0.83 | 0.94 | 36 | empty |
| 3 | 116 | 0.79 | 0.98 | 30 | empty |
| 4 | 61 | 0.76 | 0.99 | 13 | empty |
| 5 | 81 | 0.75 | 0.98 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5705 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 5672 Ų buried · 82 hydrogen bonds · protein-protein
- B–C · 5663 Ų buried · 82 hydrogen bonds · protein-protein
Compared structures
- 5JSE · Crystal structure of phiAB6 tailspike in complex with three-repeated oligosaccharides of… · 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
- Elsewhere: RCSB PDB 5JSE · PDBe 5JSE
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