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2.15 ångström crystal structure of N-acetylmuramoyl-L-alanine amidase from staphylococcus aureus.
Analyse 2.15 ångström crystal structure of N-acetylmuramoyl-L-alanine amidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T1Q
- Type
- protein
- Length
- 1,423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979
- UniProt
- Q2G222
- Ligands
- NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979 | protein | 358 | 32% helix, 18% strand | Q2G222 |
| B | N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979 | protein | 355 | 33% helix, 19% strand | Q2G222 |
| C | N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979 | protein | 357 | 32% helix, 19% strand | Q2G222 |
| D | N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979 | protein | 353 | 32% helix, 19% strand | Q2G222 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.81 | 0.87 | 66 | empty |
| 2 | 169 | 0.78 | 0.94 | 37 | empty |
| 3 | 177 | 0.77 | 0.93 | 42 | empty |
| 4 | 164 | 0.76 | 0.93 | 42 | empty |
| 5 | 181 | 0.75 | 0.92 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 444 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 366 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 149 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5T1Q · 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2G222 · AlphaFold monomer V2.0 prediction for N-acetylmuramoyl-L-alanine amidase… · a predicted model of the same protein · chain D 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 Q2G222
- Elsewhere: RCSB PDB 5T1Q · PDBe 5T1Q · UniProt Q2G222
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