Research workbench
Crystal structure of staphylococcus aureus hydrolase amia in complex with its ligand
Analyse Crystal structure of staphylococcus aureus hydrolase amia in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KNL
- Type
- protein
- Length
- 829 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional autolysin; Muramyl tetrapeptide
- EC
- 3.5.1.28, 3.2.1.96
- UniProt
- Q2FZK7
- Ligands
- MUB, OXM, NA, NH2
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional autolysin (EC 3.5.1.28, 3.2.1.96) | protein | 205 | 36% helix, 13% strand | Q2FZK7 |
| C | Bifunctional autolysin (EC 3.5.1.28, 3.2.1.96) | protein | 207 | 36% helix, 13% strand | Q2FZK7 |
| D | Bifunctional autolysin (EC 3.5.1.28, 3.2.1.96) | protein | 204 | 36% helix, 13% strand | Q2FZK7 |
| F, G | Muramyl tetrapeptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MUB · N-acetyl-alpha-muramic acid · ligand · 2 copies · chains C, F, D, G
- OXM · Oxamic acid · ligand · chains B, D
- NA · Sodium ion · metal · 8 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains C, F, G, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, D, F, G
- TAR · D(-)-tartaric acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.71 | 0.79 | 70 | empty |
| 2 | 72 | 0.69 | 0.94 | 16 | MPD |
| 3 | 227 | 0.52 | 0.76 | 24 | empty |
| 4 | 199 | 0.49 | 0.76 | 32 | NA, TAR |
| 5 | 220 | 0.48 | 0.74 | 28 | NA |
Interfaces
11 interfaces between chains.
- A–C · 793 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 791 Ų buried · 9 hydrogen bonds · protein-protein
- D–G · 344 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 342 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 310 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino (covalent ligand, D-amino acid, acetylation, nonstandard).
Compared structures
- 4KNL · Crystal structure of Staphylococcus aureus hydrolase AmiA in complex with its ligand · the same entry in another collection · chain C against C, TM-score 1.00
- Q2FZK7 · AlphaFold monomer V2.0 prediction for bifunctional autolysin (Q2FZK7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q2FZK7
- Elsewhere: RCSB PDB 4KNL · PDBe 4KNL · UniProt Q2FZK7
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