Research workbench
Class 2 of erythrocyte ankyrin-1 complex (composite MAP)
Analyse Class 2 of erythrocyte ankyrin-1 complex (composite MAP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CTE
- Type
- protein
- Length
- 4,984 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ankyrin-1; Band 3 anion transport protein; Protein 4.2; Blood group RH(CE) polypeptide…
- UniProt
- P16157, P02730, P16452, P18577, Q02094, P02724, P29972
- Ligands
- CLR, AJP, PIO, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ankyrin-1 | protein | 451 | 54% helix, 1% strand | P16157 |
| W | Band 3 anion transport protein | protein | 32 | 47% helix, 3% strand | P02730 |
| X | Protein 4.2 | protein | 657 | 18% helix, 41% strand | P16452 |
| K | Blood group RH(CE) polypeptide | protein | 380 | 71% helix, 3% strand | P18577 |
| L | Ammonium transporter rh type a | protein | 388 | 72% helix, 2% strand | Q02094 |
| Q | Ammonium transporter rh type a | protein | 390 | 73% helix, 2% strand | Q02094 |
| N, D | Glycophorin-a | protein | 40 | 63% helix, 0% strand | P02724 |
| P | Band 3 anion transport protein | protein | 804 | 54% helix, 11% strand | P02730 |
| T | Band 3 anion transport protein | protein | 814 | 54% helix, 11% strand | P02730 |
| S, O, R, M | Aquaporin-1 | protein | 247 | 70% helix, 0% strand | P29972 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 10 copies · chains L, N, P, D, T, S, O, R, M
- AJP · Digitonin · ligand · 2 copies · chains Q
- 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 P, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains P, T
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 | 237 | 0.84 | 0.96 | 41 | empty |
| 2 | 1101 | 0.84 | 0.85 | 112 | empty |
| 3 | 1114 | 0.79 | 0.81 | 108 | empty |
| 4 | 782 | 0.79 | 0.83 | 81 | empty |
| 5 | 116 | 0.78 | 0.96 | 29 | empty |
Interfaces
21 interfaces between chains.
- P–T · 3994 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 2869 Ų buried · 25 hydrogen bonds · protein-protein
- L–Q · 2704 Ų buried · 24 hydrogen bonds · protein-protein
- K–Q · 2630 Ų buried · 11 hydrogen bonds · protein-protein
- A–X · 1893 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 glycan (nonstandard, N-glycosylation).
Compared structures
- 8CTE · Class 2 of erythrocyte ankyrin-1 complex (Composite map) · the same entry in another collection · chain S against S, 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 P16157
- Every structure of UniProt P02730
- Every structure of UniProt P16452
- Every structure of UniProt P18577
- Every structure of UniProt Q02094
- Every structure of UniProt P02724
- Every structure of UniProt P29972
- Elsewhere: RCSB PDB 8CTE · PDBe 8CTE · UniProt P16157 · UniProt P02730 · UniProt P16452 · UniProt P18577 · UniProt Q02094 · UniProt P02724 · UniProt P29972
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