Research workbench
Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ank), emts derivative
Analyse Crystal structure of the ankyrin binding domain of human erythroid beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KBU
- Type
- protein
- Length
- 892 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spectrin beta chain, erythrocyte; Ankyrin-1
- UniProt
- P11277, P16157
- Ligands
- HG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spectrin beta chain, erythrocyte | protein | 285 | 88% helix, 0% strand | P11277 |
| B | Spectrin beta chain, erythrocyte | protein | 298 | 87% helix, 0% strand | P11277 |
| C | Ankyrin-1 | protein | 153 | 11% helix, 41% strand | P16157 |
| D | Ankyrin-1 | protein | 156 | 11% helix, 41% strand | P16157 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.65 | 0.76 | 59 | HG |
| 2 | 472 | 0.62 | 0.76 | 54 | HG |
| 3 | 444 | 0.59 | 0.74 | 33 | empty |
| 4 | 186 | 0.47 | 0.75 | 20 | HG |
| 5 | 164 | 0.43 | 0.74 | 24 | HG |
Interfaces
4 interfaces between chains.
- A–D · 822 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 812 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 156 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KBU · Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats… · the same entry in another collection · chain D against D, TM-score 1.00
- P11277 · AlphaFold monomer V2.0 prediction for spectrin beta chain, erythrocytic (P11277) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P16157 · AlphaFold monomer V2.0 prediction for ankyrin-1 (P16157) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P11277
- Every structure of UniProt P16157
- Elsewhere: RCSB PDB 3KBU · PDBe 3KBU · UniProt P11277 · UniProt P16157
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