MolNFT v1 · #120649 · protein
Crystal structure of the mrsd-protein a fusion protein
5H75 · Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a: “Crystal structure of the mrsd-protein a fusion protein”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.76). MolNFT v1 #120649 on GenesisL1: 3D…
- PDB
- 5H75
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a
- EC
- 4.1.1.-
- UniProt
- Q9RC23, P38507
- Ligands
- FAD
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a (EC 4.1.1.-) | protein | 212 | 50% helix, 17% strand | Q9RC23, P38507 |
| B | Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a (EC 4.1.1.-) | protein | 200 | 53% helix, 16% strand | Q9RC23, P38507 |
| C | Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a (EC 4.1.1.-) | protein | 202 | 51% helix, 15% strand | Q9RC23, P38507 |
| D | Mersacidin DECARBOXYLASE,IMMUNOGLOBULIN G-binding protein a (EC 4.1.1.-) | protein | 225 | 51% helix, 20% strand | Q9RC23, P38507 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.76 | 0.79 | 81 | FAD |
| 2 | 393 | 0.58 | 0.75 | 40 | empty |
| 3 | 224 | 0.53 | 0.77 | 30 | FAD |
| 4 | 133 | 0.46 | 0.78 | 15 | empty |
| 5 | 79 | 0.41 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–C · 704 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 630 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 520 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5H75 · Crystal structure of the MrsD-Protein A fusion protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RC23 · AlphaFold monomer V2.0 prediction for mersacidin decarboxylase (Q9RC23) · a predicted model of the same protein · chain A against A, TM-score 0.81
- 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 0.33
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 Q9RC23
- Every structure of UniProt P38507
- Elsewhere: RCSB PDB 5H75 · PDBe 5H75 · UniProt Q9RC23 · UniProt P38507
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