MolNFT v1 · #117536 · protein
Crystal form I of yfib belonging to space groups P21
5EAZ: “Crystal form I of yfib belonging to space groups P21”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.72). MolNFT v1 #117536 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EAZ
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfib
- UniProt
- Q9I4L6
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Yfib | protein | 135 | 45% helix, 20% strand | Q9I4L6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.72 | 0.82 | 49 | empty |
| 2 | 377 | 0.64 | 0.79 | 35 | empty |
| 3 | 168 | 0.61 | 0.83 | 34 | empty |
| 4 | 128 | 0.41 | 0.75 | 21 | empty |
| 5 | 135 | 0.41 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1174 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 323 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5EAZ · crystal form I of YfiB belonging to space groups P21 · 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 Q9I4L6
- Elsewhere: RCSB PDB 5EAZ · PDBe 5EAZ · UniProt Q9I4L6
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