MolNFT v1 · #115168 · protein
Fusion protein of MBP3-16 and B4 domain of protein a from staphylococcal aureus with chemical cross-linker ey-cbs
5CBN · Maltose-binding periplasmic protein: “Fusion protein of MBP3-16 and B4 domain of protein a from staphylococcal aureus with chemical cross-linker…”. X-ray diffraction, 1 ligand (EYC), 3 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 5CBN
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; MBP3-16,IMMUNOGLOBULIN G-binding protein a
- UniProt
- P0AEX9, P38507
- Ligands
- EYC
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Maltose-binding periplasmic protein | protein | 362 | 46% helix, 18% strand | P0AEX9 |
| A | MBP3-16,IMMUNOGLOBULIN G-binding protein a | protein | 176 | 61% helix, 0% strand | P38507 |
Ligands and binding sites
- EYC · 2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid} · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.69 | 0.82 | 37 | empty |
| 2 | 259 | 0.56 | 0.77 | 35 | empty |
| 3 | 115 | 0.40 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- B–A · 666 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5CBN · Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with… · the same entry in another collection · chain B against B, TM-score 1.00
- P38507 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P38507) · a predicted model of the same protein · chain A against A, TM-score 0.31
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 P0AEX9
- Every structure of UniProt P38507
- Elsewhere: RCSB PDB 5CBN · PDBe 5CBN · UniProt P0AEX9 · UniProt P38507
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