MolNFT v1 · #167344 · protein
Klebsiella oxytoca npsa N-terminal subdomain in complex with 3- hydroxyanthranilyl-amsn
6VHX · Npsa adenylation domain: “Klebsiella oxytoca npsa N-terminal subdomain in complex with 3- hydroxyanthranilyl-amsn”. X-ray diffraction, 3 ligands (QXG, CL, BR), 4 pockets (best druggability 0.78). MolNFT v1 #167344 on GenesisL1: 3D…
- PDB
- 6VHX
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npsa adenylation domain
- UniProt
- A0A2U4DY99
- Ligands
- QXG, CL, BR
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npsa adenylation domain | protein | 389 | 31% helix, 30% strand | A0A2U4DY99 |
| B | Npsa adenylation domain | protein | 389 | 32% helix, 30% strand | A0A2U4DY99 |
Ligands and binding sites
- QXG · 5'-{[(2-amino-3-hydroxybenzene-1-carbonyl) sulfamoyl]amino}-5'-deoxyadenosine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- BR · Bromide ion · ion · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.78 | 0.85 | 77 | QXG, BR |
| 2 | 393 | 0.76 | 0.86 | 58 | QXG, CL |
| 3 | 133 | 0.51 | 0.80 | 22 | empty |
| 4 | 67 | 0.27 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 978 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6VHX · Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hydroxyanthranilyl-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 6VHX · PDBe 6VHX · UniProt A0A2U4DY99
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