MolNFT v1 · #143551 · protein
Apo yiua crystal form 2
6B2Y · Solute-binding periplasmic protein of IRON/SIDEROPHORE ABC…: “Apo yiua crystal form 2”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.71). MolNFT v1 #143551 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6B2Y
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Solute-binding periplasmic protein of IRON/SIDEROPHORE ABC transporter
- UniProt
- Q8D027
- Ligands
- NA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Solute-binding periplasmic protein of IRON/SIDEROPHORE ABC transporter | protein | 338 | 42% helix, 17% strand | Q8D027 |
| B | Solute-binding periplasmic protein of IRON/SIDEROPHORE ABC transporter | protein | 331 | 44% helix, 16% strand | Q8D027 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.71 | 0.80 | 57 | NA |
| 2 | 260 | 0.59 | 0.79 | 33 | empty |
| 3 | 108 | 0.44 | 0.78 | 19 | empty |
| 4 | 97 | 0.44 | 0.79 | 20 | empty |
| 5 | 71 | 0.41 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1074 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6B2Y · Apo YiuA Crystal Form 2 · 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 Q8D027
- Elsewhere: RCSB PDB 6B2Y · PDBe 6B2Y · UniProt Q8D027
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