MolNFT v1 · #40857 · protein
Ceruloplasmin revisited: structural and functional roles of various metal cation binding sites
2J5W: “Ceruloplasmin revisited: structural and functional roles of various metal cation binding sites”. X-ray diffraction, 6 ligands (NAG, CU, NA), 16 pockets (best druggability 0.86). MolNFT v1 #40857 on GenesisL1: 3D structure, binding…
- PDB
- 2J5W
- Type
- protein
- Length
- 1,029 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ceruloplasmin
- EC
- 1.16.3.1
- UniProt
- P00450
- Ligands
- NAG, CU, NA, CA, O, OXY
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ceruloplasmin (EC 1.16.3.1) | protein | 1029 | 14% helix, 39% strand | P00450 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CU · Copper (II) ion · metal · 7 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- O · Oxygen atom · ion · chains A
- OXY · Oxygen molecule · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.86 | 0.91 | 63 | GOL |
| 2 | 567 | 0.66 | 0.76 | 72 | CU, GOL |
| 3 | 266 | 0.62 | 0.80 | 36 | empty |
| 4 | 289 | 0.57 | 0.77 | 40 | empty |
| 5 | 201 | 0.55 | 0.79 | 35 | empty |
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2J5W · Ceruloplasmin revisited: structural and functional roles of various metal cation binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P00450 · AlphaFold monomer V2.0 prediction for ceruloplasmin (P00450) · a predicted model of the same protein · chain A 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 P00450
- Elsewhere: RCSB PDB 2J5W · PDBe 2J5W · UniProt P00450
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