Research workbench
HUMAN CD53
Analyse HUMAN CD53 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVG
- Type
- protein
- Length
- 883 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein, leukocyte surface antigen CD53 chimera
- UniProt
- P42212, P19397
- Ligands
- CRO, NAG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Green fluorescent protein, leukocyte surface antigen CD53 chimera | protein | 443 | 39% helix, 27% strand | P42212, P19397 |
| B | Green fluorescent protein, leukocyte surface antigen CD53 chimera | protein | 440 | 40% helix, 27% strand | P42212, P19397 |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.83 | 0.84 | 63 | OLC |
| 2 | 101 | 0.76 | 0.96 | 25 | CRO |
| 3 | 104 | 0.75 | 0.96 | 22 | CRO |
| 4 | 189 | 0.59 | 0.81 | 26 | empty |
| 5 | 130 | 0.56 | 0.83 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1787 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor, 4 disulfide, 2 glycan (chromophore, disulfide, N-glycosylation).
Compared structures
- 6WVG · human CD53 · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain B against A, TM-score 0.52
- P19397 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD53 (P19397) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 P42212
- Every structure of UniProt P19397
- Elsewhere: RCSB PDB 6WVG · PDBe 6WVG · UniProt P42212 · UniProt P19397
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