MolNFT v1 · #38279 · protein
Crystal structure of a murine Fab in complex with an 11 residue peptide derived from staphylococcal nuclease
2GSI · Immunoglobulin (kappa) light chain: “Crystal structure of a murine Fab in complex with an 11 residue peptide derived from staphylococcal nuclease”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 2GSI
- Type
- protein
- Length
- 1,752 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin (kappa) light chain; Immunoglobulin (gamma) heavy chain (vh + CH1…
- EC
- 3.1.31.1
- UniProt
- Q6PF95, Q8NXI6
- Ligands
- NA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Immunoglobulin (kappa) light chain | protein | 215 | 6% helix, 52% strand | — |
| B | Immunoglobulin (gamma) heavy chain (vh + CH1 fragment) | protein | 210 | 4% helix, 57% strand | Q6PF95 |
| D | Immunoglobulin (gamma) heavy chain (vh + CH1 fragment) | protein | 215 | 6% helix, 56% strand | Q6PF95 |
| F | Immunoglobulin (gamma) heavy chain (vh + CH1 fragment) | protein | 214 | 7% helix, 54% strand | Q6PF95 |
| H | Immunoglobulin (gamma) heavy chain (vh + CH1 fragment) | protein | 213 | 8% helix, 54% strand | Q6PF95 |
| X, Y | Thermonuclease (EC 3.1.31.1) | protein | 11 | 0% helix, 9% strand | Q8NXI6 |
| Z | Thermonuclease (EC 3.1.31.1) | protein | 8 | 0% helix, 25% strand | Q8NXI6 |
| W | Thermonuclease (EC 3.1.31.1) | protein | 10 | 0% helix, 20% strand | Q8NXI6 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains B, D, E, Y, F, G, H, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.74 | 0.98 | 19 | NA |
| 2 | 777 | 0.73 | 0.78 | 75 | empty |
| 3 | 808 | 0.73 | 0.78 | 75 | empty |
| 4 | 362 | 0.72 | 0.84 | 55 | empty |
| 5 | 55 | 0.71 | 0.98 | 21 | empty |
Interfaces
25 interfaces between chains.
- G–H · 1811 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1769 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1735 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1721 Ų buried · 14 hydrogen bonds · protein-protein
- F–Y · 479 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2GSI · Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from… · the same entry in another collection · chain Y against Y, TM-score 1.00
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 Q6PF95
- Every structure of UniProt Q8NXI6
- Elsewhere: RCSB PDB 2GSI · PDBe 2GSI · UniProt Q6PF95 · UniProt Q8NXI6
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