Research workbench
NB22-LBT
Analyse NB22-LBT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y1R
- Type
- protein
- Length
- 685 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB22-lbt
- Ligands
- TB, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NB22-lbt | protein | 141 | 11% helix, 48% strand | — |
| B | NB22-lbt | protein | 129 | 8% helix, 49% strand | — |
| D | NB22-lbt | protein | 139 | 10% helix, 41% strand | — |
| E | NB22-lbt | protein | 135 | 8% helix, 45% strand | — |
Ligands and binding sites
- TB · Terbium(iii) ion · metal · 9 copies · chains A, D, B, C, E
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.80 | 0.82 | 86 | empty |
| 2 | 1104 | 0.77 | 0.79 | 101 | empty |
| 3 | 63 | 0.32 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–E · 687 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 608 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6Y1R · Nb22-LBT · 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
- Elsewhere: RCSB PDB 6Y1R · PDBe 6Y1R
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