Research workbench
Crystal structure of outer membrane protein porb from neisseria meningitidis in complex with AMP-pnp
Analyse Crystal structure of outer membrane protein porb from neisseria meningitidis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZU
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein
- Ligands
- ANP
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Outer membrane protein | protein | 341 | 6% helix, 58% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.70 | 0.76 | 86 | ANP |
| 2 | 142 | 0.67 | 0.88 | 23 | empty |
| 3 | 171 | 0.45 | 0.75 | 31 | empty |
| 4 | 107 | 0.37 | 0.75 | 17 | empty |
Compared structures
- 3VZU · Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex… · the same entry in another collection · chain X against X, 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
- Elsewhere: RCSB PDB 3VZU · PDBe 3VZU
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