Research workbench
Y177F variant of S. enterica rmla
Analyse Y177F variant of S. enterica rmla in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MP5
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Y177F variant of S. enterica rmla bound to udp-glucose
- EC
- 2.7.7.24
- UniProt
- Q9F7G8
- Ligands
- UPG
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Y177F variant of S. enterica rmla bound to udp-glucose (EC 2.7.7.24) | protein | 289 | 36% helix, 21% strand | Q9F7G8 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.80 | 0.81 | 111 | empty |
| 2 | 986 | 0.78 | 0.80 | 85 | UPG |
| 3 | 452 | 0.75 | 0.84 | 47 | UPG |
| 4 | 59 | 0.75 | 0.99 | 17 | empty |
| 5 | 470 | 0.74 | 0.83 | 40 | UPG |
Interfaces
4 interfaces between chains.
- C–D · 1428 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1404 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1376 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1MP5 · Y177F VARIANT OF S. ENTERICA RmlA · 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 Q9F7G8
- Elsewhere: RCSB PDB 1MP5 · PDBe 1MP5 · UniProt Q9F7G8
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