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Crystal structure of a pantoate-beta-alanine ligase from neisseria gonorrhoeae with bound amppnp and alanine
Analyse Crystal structure of a pantoate-beta-alanine ligase from neisseria gonorrhoeae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UCR
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate synthetase
- EC
- 6.3.2.1
- UniProt
- B4RKE7
- Ligands
- ALA, ANP, MG
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate synthetase (EC 6.3.2.1) | protein | 271 | 42% helix, 23% strand | B4RKE7 |
| B | Pantothenate synthetase (EC 6.3.2.1) | protein | 266 | 42% helix, 23% strand | B4RKE7 |
Ligands and binding sites
- ALA · Alanine · ligand · 3 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.83 | 0.91 | 59 | ANP, ALA, MG |
| 2 | 512 | 0.76 | 0.84 | 59 | ANP, ALA |
| 3 | 245 | 0.57 | 0.78 | 29 | empty |
| 4 | 91 | 0.38 | 0.76 | 20 | empty |
| 5 | 50 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5UCR · Crystal Structure of a Pantoate-beta-alanine Ligase from Neisseria gonorrhoeae with bound… · 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 B4RKE7
- Elsewhere: RCSB PDB 5UCR · PDBe 5UCR · UniProt B4RKE7
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