Research workbench
N-acetylneuraminate lyase from methicillin-resistant staphylococcus aureus with bound sialic acid alditol
Analyse N-acetylneuraminate lyase from methicillin-resistant staphylococcus aureus with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZD
- Type
- protein
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q2FJU9
- Ligands
- RCJ
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 284 | 53% helix, 14% strand | Q2FJU9 |
Ligands and binding sites
- RCJ · (2~{S},4~{S},5~{R},6~{R},7~{S},8~{R})-5-acetamido-2,4, 6,7,8,9-hexakis(oxidanyl)nonanoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.75 | 0.92 | 27 | empty |
| 2 | 168 | 0.71 | 0.89 | 28 | empty |
| 3 | 367 | 0.62 | 0.77 | 40 | RCJ |
| 4 | 341 | 0.62 | 0.78 | 38 | RCJ |
| 5 | 404 | 0.62 | 0.76 | 46 | RCJ |
Interfaces
4 interfaces between chains.
- B–D · 1437 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1376 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1208 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5KZD · N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus with bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FJU9 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q2FJU9) · a predicted model of the same protein · 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 Q2FJU9
- Elsewhere: RCSB PDB 5KZD · PDBe 5KZD · UniProt Q2FJU9
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