MolNFT v1 · #158146 · protein
Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of streptococcal protein G (L12H, T16L, V29H, Y33H, N37L)-apo
6NL9 · Immunoglobulin G-binding protein G: “Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of…”. X-ray diffraction, 2 ligands (NA, MG), 3 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 6NL9
- Type
- protein
- Length
- 224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein G
- UniProt
- P19909
- Ligands
- NA, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Immunoglobulin G-binding protein G | protein | 56 | 25% helix, 43% strand | P19909 |
Ligands and binding sites
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 | 546 | 0.69 | 0.79 | 49 | empty |
| 2 | 399 | 0.64 | 0.79 | 34 | empty |
| 3 | 132 | 0.46 | 0.78 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–C · 477 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 456 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 260 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 248 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NL9 · Crystal structure of de novo designed metal-controlled dimer of mutant B1… · the same entry in another collection · chain A against A, TM-score 1.00
- P19909 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein G (P19909) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P19909
- Elsewhere: RCSB PDB 6NL9 · PDBe 6NL9 · UniProt P19909
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