Research workbench
Crystal structure of full-length lpoa, monoclinic form 1, from haemophilus influenzae
Analyse Crystal structure of full-length lpoa, monoclinic form 1, from haemophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VBG
- Type
- protein
- Length
- 543 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein activator lpoa
- UniProt
- P45299
- Ligands
- CL
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein activator lpoa | protein | 543 | 55% helix, 13% strand | P45299 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.59 | 0.87 | 21 | CL |
| 2 | 314 | 0.57 | 0.76 | 36 | empty |
| 3 | 171 | 0.45 | 0.75 | 22 | empty |
| 4 | 50 | 0.37 | 0.80 | 12 | empty |
| 5 | 74 | 0.31 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 11 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5VBG · Crystal Structure of full-length LpoA, Monoclinic form 1, from Haemophilus influenzae · the same entry in another collection · chain A against A, TM-score 1.00
- P45299 · AlphaFold monomer V2.0 prediction for penicillin-binding protein activator lpoa (P45299) · a predicted model of the same protein · chain A 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 P45299
- Elsewhere: RCSB PDB 5VBG · PDBe 5VBG · UniProt P45299
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