MolNFT v1 · #72520 · protein
Crystal structure of E. COLI O157:H7 effector protein nlel
3NB2 · Secreted effector protein: “Crystal structure of E. COLI O157:H7 effector protein nlel”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.86). MolNFT v1 #72520 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3NB2
- Type
- protein
- Length
- 2,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted effector protein
- UniProt
- Q8X5G6
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Secreted effector protein | protein | 612 | 43% helix, 9% strand | Q8X5G6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, C, B, D
- GOL · Glycerol · additive · 29 copies · chains A, C, B, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, C, B, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.86 | 0.87 | 95 | GOL, DTT |
| 2 | 432 | 0.82 | 0.89 | 52 | GOL, SO4 |
| 3 | 574 | 0.76 | 0.83 | 63 | GOL, SO4 |
| 4 | 344 | 0.76 | 0.87 | 39 | GOL |
| 5 | 384 | 0.75 | 0.85 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2172 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1945 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 250 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NB2 · Crystal structure of E. coli O157:H7 effector protein NleL · 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 Q8X5G6
- Elsewhere: RCSB PDB 3NB2 · PDBe 3NB2 · UniProt Q8X5G6
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