MolNFT v1 · #10843 · protein
Structure of gliding protein-mglb from thermus thermophilus HB8
1J3W · Giding protein-mglb: “Structure of gliding protein-mglb from thermus thermophilus HB8”. X-ray diffraction, 2 ligands (MG, SO4), 2 pockets (best druggability 0.74). MolNFT v1 #10843 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1J3W
- Type
- protein
- Length
- 535 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Giding protein-mglb
- UniProt
- Q9X9L0
- Ligands
- MG, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Giding protein-mglb | protein | 134 | 45% helix, 22% strand | Q9X9L0 |
| B | Giding protein-mglb | protein | 135 | 44% helix, 22% strand | Q9X9L0 |
| C, D | Giding protein-mglb | protein | 133 | 46% helix, 23% strand | Q9X9L0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.74 | 0.83 | 57 | empty |
| 2 | 60 | 0.39 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1334 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 259 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1J3W · Structure of Gliding protein-mglB from Thermus Thermophilus HB8 · 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 Q9X9L0
- Elsewhere: RCSB PDB 1J3W · PDBe 1J3W · UniProt Q9X9L0
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