MolNFT v1 · #189040 · protein
Band 3-I-tm local refinement from erythrocyte ankyrin-1 complex consensus reconstruction
7V07 · Glycophorin-a: “Band 3-I-tm local refinement from erythrocyte ankyrin-1 complex consensus reconstruction”. Electron microscopy, 7 ligands (CLR, PLC, PIO), 15 pockets (best druggability 0.77). MolNFT v1 #189040 on GenesisL1: 3D…
- PDB
- 7V07
- Type
- protein
- Length
- 1,114 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycophorin-a; Band 3 anion transport protein
- UniProt
- P02724, P02730
- Ligands
- CLR, PLC, PIO, NAG, MAN, BMA, FUC
- Pockets
- 15 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Glycophorin-a | protein | 40 | 63% helix, 0% strand | P02724 |
| C, E | Band 3 anion transport protein | protein | 517 | 66% helix, 3% strand | P02730 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains B, C, D, E
- PLC · Diundecyl phosphatidyl choline · ligand · 2 copies · chains C, E
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, E
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.77 | 0.83 | 65 | empty |
| 2 | 583 | 0.77 | 0.83 | 67 | empty |
| 3 | 327 | 0.70 | 0.84 | 48 | empty |
| 4 | 319 | 0.66 | 0.81 | 51 | empty |
| 5 | 461 | 0.60 | 0.73 | 45 | PLC |
Interfaces
3 interfaces between chains.
- C–E · 1301 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1026 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 972 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 7V07 · Band 3-I-TM local refinement from erythrocyte ankyrin-1 complex consensus reconstruction · the same entry in another collection · chain E against E, TM-score 1.00
- P02730 · AlphaFold monomer V2.0 prediction for band 3 anion transport protein (P02730) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P02724 · AlphaFold monomer V2.0 prediction for glycophorin-a (P02724) · a predicted model of the same protein · chain B against A, TM-score 0.61
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 P02724
- Every structure of UniProt P02730
- Elsewhere: RCSB PDB 7V07 · PDBe 7V07 · UniProt P02724 · UniProt P02730
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