Research workbench
Crystal structure of A58P, DEL(N59), and loop 7 truncated mutant of 3- deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
Analyse Crystal structure of A58P, DEL(N59), and loop 7 truncated mutant of 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3STG
- Type
- protein
- Length
- 1,046 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- Q9JZ55
- Ligands
- CL
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 260 | 42% helix, 21% strand | Q9JZ55 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 268 | 42% helix, 20% strand | Q9JZ55 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 258 | 43% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.70 | 0.79 | 68 | CL |
| 2 | 488 | 0.67 | 0.78 | 63 | CL |
| 3 | 415 | 0.66 | 0.79 | 61 | CL |
| 4 | 408 | 0.63 | 0.78 | 59 | CL |
| 5 | 171 | 0.63 | 0.84 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1794 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1728 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 1435 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1303 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 221 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3STG · Crystal structure of A58P, DEL(N59), and loop 7 truncated mutant of… · 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 Q9JZ55
- Elsewhere: RCSB PDB 3STG · PDBe 3STG · UniProt Q9JZ55
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