Research workbench
Crystal structure of human adenovirus 52 short fiber knob in complex with 2-O-methyl-5-N-acetylneuraminic acid
Analyse Crystal structure of human adenovirus 52 short fiber knob in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XL8
- Type
- protein
- Length
- 499 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber-1
- UniProt
- A0MK70
- Ligands
- MNA, TAM, GLU, ALA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber-1 | protein | 171 | 10% helix, 43% strand | A0MK70 |
| B | Fiber-1 | protein | 161 | 9% helix, 45% strand | A0MK70 |
| C | Fiber-1 | protein | 167 | 8% helix, 47% strand | A0MK70 |
Ligands and binding sites
- MNA · 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid · ligand · 2 copies · chains A, B, C
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- GLU · Glutamic acid · ligand · chains B
- ALA · Alanine · ligand · chains B
- GOL · Glycerol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.81 | 0.97 | 31 | empty |
| 2 | 71 | 0.30 | 0.74 | 17 | empty |
| 3 | 64 | 0.28 | 0.73 | 20 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1053 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1039 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4XL8 · Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with… · the same entry in another collection · chain B against B, 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 A0MK70
- Elsewhere: RCSB PDB 4XL8 · PDBe 4XL8 · UniProt A0MK70
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