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Crystal structure of the N-terminal lysm domains from the putative NLPC/P60 D,L endopeptidase from T. thermophilus bound to N-acetyl- chitohexaose
Analyse Crystal structure of the N-terminal lysm domains from the putative NLPC/P60 D,L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UZ3
- Type
- protein
- Length
- 240 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell wall-binding endopeptidase-related protein
- UniProt
- Q5SLM7
- Ligands
- NAG, NDG, SO4
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell wall-binding endopeptidase-related protein | protein | 99 | 34% helix, 12% strand | Q5SLM7 |
| B | Cell wall-binding endopeptidase-related protein | protein | 94 | 31% helix, 13% strand | Q5SLM7 |
| C | Cell wall-binding endopeptidase-related protein | protein | 47 | 34% helix, 13% strand | Q5SLM7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.55 | 0.74 | 54 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 406 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4UZ3 · Crystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L… · 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 Q5SLM7
- Elsewhere: RCSB PDB 4UZ3 · PDBe 4UZ3 · UniProt Q5SLM7
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