MolNFT v1 · #60886 · protein
Structure of purlqs from thermotoga maritima
3D54 · Phosphoribosylformylglycinamidine synthase II: “Structure of purlqs from thermotoga maritima”. X-ray diffraction, 2 ligands (ADP, NA), 20 pockets (best druggability 0.85). MolNFT v1 #60886 on GenesisL1: 3D structure, binding sites…
- PDB
- 3D54
- Type
- protein
- Length
- 2,877 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine synthase II; Formylglycinamide ribonucleotide…
- EC
- 6.3.5.3
- UniProt
- Q9X0X3, Q9X0X1, Q9X0X2
- Ligands
- ADP, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Phosphoribosylformylglycinamidine synthase II (EC 6.3.5.3) | protein | 583 | 29% helix, 26% strand | Q9X0X3 |
| B, C, F, G, J, K | Formylglycinamide ribonucleotide amidotransferase (EC 6.3.5.3) | protein | 82 | 34% helix, 35% strand | Q9X0X1 |
| D, H, L | Phosphoribosylformylglycinamidine synthase 1 (EC 6.3.5.3) | protein | 212 | 23% helix, 27% strand | Q9X0X2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, I, E
- NA · Sodium ion · metal · 3 copies · chains A, I, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.85 | 0.95 | 56 | ADP |
| 2 | 310 | 0.85 | 0.95 | 56 | ADP |
| 3 | 301 | 0.84 | 0.94 | 52 | ADP |
| 4 | 938 | 0.81 | 0.83 | 72 | empty |
| 5 | 998 | 0.80 | 0.82 | 69 | empty |
Interfaces
22 interfaces between chains.
- J–K · 1463 Ų buried · 31 hydrogen bonds · protein-protein
- F–G · 1458 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1454 Ų buried · 32 hydrogen bonds · protein-protein
- I–L · 1388 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1387 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 3D54 · Structure of PurLQS from Thermotoga maritima · the same entry in another collection · chain L against L, 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 Q9X0X3
- Every structure of UniProt Q9X0X1
- Every structure of UniProt Q9X0X2
- Elsewhere: RCSB PDB 3D54 · PDBe 3D54 · UniProt Q9X0X3 · UniProt Q9X0X1 · UniProt Q9X0X2
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