Research workbench
Cryo-EM structure of human band 3-protein 4.2 complex in diagonal conformation
Analyse Cryo-EM structure of human band 3-protein 4.2 complex in diagonal conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TVZ
- Type
- protein
- Length
- 2,340 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Band 3 anion transport protein; Protein 4.2
- UniProt
- P02730, P16452
- Ligands
- CLR, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Band 3 anion transport protein | protein | 850 | 52% helix, 10% strand | P02730 |
| B | Band 3 anion transport protein | protein | 825 | 52% helix, 10% strand | P02730 |
| E | Protein 4.2 | protein | 665 | 17% helix, 40% strand | P16452 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.86 | 0.88 | 116 | empty |
| 2 | 533 | 0.78 | 0.84 | 44 | LMT |
| 3 | 724 | 0.78 | 0.82 | 70 | LMT |
| 4 | 704 | 0.77 | 0.82 | 57 | empty |
| 5 | 854 | 0.76 | 0.80 | 101 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4133 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2066 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 7TVZ · Cryo-EM structure of human band 3-protein 4.2 complex in diagonal conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P16452 · AlphaFold monomer V2.0 prediction for protein 4.2 (P16452) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P02730 · AlphaFold monomer V2.0 prediction for band 3 anion transport protein (P02730) · a predicted model of the same protein · chain B against A, TM-score 0.65
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 P02730
- Every structure of UniProt P16452
- Elsewhere: RCSB PDB 7TVZ · PDBe 7TVZ · UniProt P02730 · UniProt P16452
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