Research workbench
Crystal structure of a putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101) from parabacteroides distasonis atcc 8503 at 1.91 a resolution
Analyse Crystal structure of a putative phosphoribosylformylglycinamidine cyclo-ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MDO
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphoribosylformylglycinamidine cyclo-ligase
- UniProt
- A6LDR8
- Ligands
- CA, CL
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phosphoribosylformylglycinamidine cyclo-ligase | protein | 365 | 36% helix, 25% strand | A6LDR8 |
| B | Putative phosphoribosylformylglycinamidine cyclo-ligase | protein | 363 | 35% helix, 26% strand | A6LDR8 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B
- PGE · Triethylene glycol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B
- P6G · Hexaethylene glycol · additive · chains A
- CAC · Cacodylate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.62 | 0.82 | 30 | empty |
| 2 | 185 | 0.61 | 0.83 | 29 | empty |
| 3 | 294 | 0.57 | 0.77 | 49 | CA, ACT, PGE |
| 4 | 216 | 0.50 | 0.76 | 38 | CA, PGE |
| 5 | 62 | 0.48 | 0.85 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1998 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3MDO · Crystal structure of a Putative phosphoribosylformylglycinamidine cyclo-ligase (BDI_2101)… · 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 A6LDR8
- Elsewhere: RCSB PDB 3MDO · PDBe 3MDO · UniProt A6LDR8
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