MolNFT v1 · #97430 · protein
Structure of an early native-like intermediate of BETA2-microglobulin amyloidosis
4KDT · NANOBODY24: “Structure of an early native-like intermediate of BETA2-microglobulin amyloidosis”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.61). MolNFT v1 #97430 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KDT
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NANOBODY24; Beta-2-microglobulin
- UniProt
- P61769
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NANOBODY24 | protein | 129 | 10% helix, 47% strand | — |
| B | NANOBODY24 | protein | 128 | 11% helix, 46% strand | — |
| C | Beta-2-microglobulin | protein | 93 | 3% helix, 55% strand | P61769 |
| D | Beta-2-microglobulin | protein | 95 | 0% helix, 54% strand | P61769 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B, C
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.61 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–D · 730 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 723 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 718 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4KDT · Structure of an early native-like intermediate of beta2-microglobulin amyloidosis · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 P61769
- Elsewhere: RCSB PDB 4KDT · PDBe 4KDT · UniProt P61769
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