Research workbench
Klebsiella oxytoca npsa N-terminal subdomain in complex with 3- hydroxybenzoyl-amsn
Analyse Klebsiella oxytoca npsa N-terminal subdomain in complex with 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VHW
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npsa adenylation domain
- UniProt
- A0A2U4DY99
- Ligands
- R2V, CL, BR
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npsa adenylation domain | protein | 396 | 30% helix, 29% strand | A0A2U4DY99 |
| B | Npsa adenylation domain | protein | 392 | 31% helix, 30% strand | A0A2U4DY99 |
Ligands and binding sites
- R2V · 5'-deoxy-5'-{[(3-hydroxybenzene-1-carbonyl) sulfamoyl]amino}adenosine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- BR · Bromide ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.79 | 0.83 | 85 | R2V |
| 2 | 724 | 0.79 | 0.83 | 88 | BR, R2V, PEG, CL |
| 3 | 166 | 0.56 | 0.81 | 24 | empty |
| 4 | 64 | 0.32 | 0.75 | 14 | empty |
| 5 | 51 | 0.24 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 953 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6VHW · Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hydroxybenzoyl-AMSN · 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 A0A2U4DY99
- Elsewhere: RCSB PDB 6VHW · PDBe 6VHW · UniProt A0A2U4DY99
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