MolNFT v1 · #113292 · protein
S.ENTERICA hisa mutant D7N, D10G, DUP13-15, Q24L, G102A
5AB3 · 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)…: “S.ENTERICA hisa mutant D7N, D10G, DUP13-15, Q24L, G102A”. X-ray diffraction, 2 ligands (2ER, NA), 8 pockets (best druggability 0.80). MolNFT v1 #113292 on GenesisL1: 3D structure…
- PDB
- 5AB3
- Type
- protein
- Length
- 721 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide…
- EC
- 5.3.1.16
- UniProt
- V7IJE3
- Ligands
- 2ER, NA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16) | protein | 241 | 41% helix, 26% strand | V7IJE3 |
| B | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16) | protein | 237 | 41% helix, 27% strand | V7IJE3 |
| C | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16) | protein | 243 | 40% helix, 26% strand | V7IJE3 |
Ligands and binding sites
- 2ER · [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[[(Z)-[(3R,4R)-3,4-dihydroxy-2-oxo-5-phosphonooxy-pentyl]iminomethyl]amino]imidazol-1-yl]-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.80 | 0.87 | 53 | 2ER |
| 2 | 698 | 0.80 | 0.84 | 97 | NA |
| 3 | 474 | 0.79 | 0.87 | 53 | 2ER |
| 4 | 502 | 0.79 | 0.86 | 55 | 2ER |
| 5 | 322 | 0.55 | 0.75 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1064 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 666 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5AB3 · S.enterica HisA mutant D7N, D10G, dup13-15, Q24L, G102A · 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 V7IJE3
- Elsewhere: RCSB PDB 5AB3 · PDBe 5AB3 · UniProt V7IJE3
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