MolNFT v1 · #167346 · protein
Klebsiella oxytoca npsa N-terminal subdomain in complex with anthranilyl-amsn
6VHZ · Npsa adenylation domain: “Klebsiella oxytoca npsa N-terminal subdomain in complex with anthranilyl-amsn”. X-ray diffraction, 3 ligands (QXP, CL, BR), 3 pockets (best druggability 0.80). MolNFT v1 #167346 on GenesisL1: 3D structure…
- PDB
- 6VHZ
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npsa adenylation domain
- UniProt
- A0A2U4DY99
- Ligands
- QXP, CL, BR
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npsa adenylation domain | protein | 379 | 31% helix, 28% strand | A0A2U4DY99 |
| B | Npsa adenylation domain | protein | 385 | 32% helix, 30% strand | A0A2U4DY99 |
Ligands and binding sites
- QXP · 5'-{[(benzenecarbonyl)sulfamoyl]amino}-5'-deoxyadenosine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.80 | 0.81 | 99 | QXP, CL, BR |
| 2 | 627 | 0.73 | 0.80 | 87 | QXP, CL |
| 3 | 158 | 0.49 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6VHZ · Klebsiella oxytoca NpsA N-terminal subdomain in complex with anthranilyl-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 6VHZ · PDBe 6VHZ · UniProt A0A2U4DY99
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