Research workbench
Local refinement of rh trimer, glycophorin B and BAND3-III transmembrane region, class 1A of erythrocyte ankyrin-1 complex
Analyse Local refinement of rh trimer, glycophorin B and BAND3-III transmembrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CRT
- Type
- protein
- Length
- 2,305 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blood group RH(CE) polypeptide; Ammonium transporter rh type a; Glycophorin-B…
- UniProt
- P18577, Q02094, P06028, P02724, P02730
- Ligands
- CLR, NAG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Blood group RH(CE) polypeptide | protein | 380 | 73% helix, 2% strand | P18577 |
| L | Ammonium transporter rh type a | protein | 388 | 71% helix, 2% strand | Q02094 |
| Q | Ammonium transporter rh type a | protein | 390 | 72% helix, 2% strand | Q02094 |
| P | Glycophorin-B | protein | 33 | 94% helix, 0% strand | P06028 |
| B, D | Glycophorin-a | protein | 40 | 63% helix, 0% strand | P02724 |
| C, E | Band 3 anion transport protein | protein | 517 | 65% helix, 3% strand | P02730 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, E
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 | 655 | 0.77 | 0.82 | 64 | empty |
| 2 | 674 | 0.76 | 0.81 | 72 | empty |
| 3 | 71 | 0.75 | 0.98 | 21 | empty |
| 4 | 380 | 0.68 | 0.81 | 58 | empty |
| 5 | 325 | 0.68 | 0.82 | 48 | empty |
Interfaces
9 interfaces between chains.
- K–L · 2889 Ų buried · 19 hydrogen bonds · protein-protein
- L–Q · 2713 Ų buried · 26 hydrogen bonds · protein-protein
- K–Q · 2534 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1296 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 978 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 8CRT · Local refinement of Rh trimer, glycophorin B and Band3-III transmembrane region, class 1a… · the same entry in another collection · chain E against E, TM-score 1.00
- Q02094 · AlphaFold monomer V2.0 prediction for ammonium transporter rh type a (Q02094) · a predicted model of the same protein · chain L against A, TM-score 0.99
- 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
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 P18577
- Every structure of UniProt Q02094
- Every structure of UniProt P06028
- Every structure of UniProt P02724
- Every structure of UniProt P02730
- Elsewhere: RCSB PDB 8CRT · PDBe 8CRT · UniProt P18577 · UniProt Q02094 · UniProt P06028 · UniProt P02724 · UniProt P02730
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