Research workbench
Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
Analyse Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OQJ
- Type
- protein
- Length
- 1,814 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2G12 light chain; Fab 2G12 heavy chain; Peptide 2G12.1 (acppshvldmrsgtclaaegk)
- UniProt
- Q6PIH4, Q6N089
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Fab 2G12 light chain | protein | 211 | 7% helix, 55% strand | Q6PIH4 |
| B, E, H, K | Fab 2G12 heavy chain | protein | 224 | 8% helix, 51% strand | Q6N089 |
| C | Peptide 2G12.1 (acppshvldmrsgtclaaegk) | protein | 18 | 0% helix, 33% strand | — |
| F | Peptide 2G12.1 (acppshvldmrsgtclaaegk) | protein | 20 | 0% helix, 40% strand | — |
| I | Peptide 2G12.1 (acppshvldmrsgtclaaegk) | protein | 17 | 0% helix, 35% strand | — |
| L | Peptide 2G12.1 (acppshvldmrsgtclaaegk) | protein | 19 | 0% helix, 42% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.85 | 0.88 | 72 | empty |
| 2 | 907 | 0.75 | 0.78 | 98 | empty |
| 3 | 876 | 0.73 | 0.78 | 93 | empty |
| 4 | 839 | 0.73 | 0.78 | 79 | empty |
| 5 | 564 | 0.72 | 0.80 | 55 | empty |
Interfaces
28 interfaces between chains.
- D–E · 1015 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1014 Ų buried · 8 hydrogen bonds · protein-protein
- G–K · 1013 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 8 hydrogen bonds · protein-protein
- J–K · 1009 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2OQJ · Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1 · the same entry in another collection · chain A against A, 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 Q6PIH4
- Every structure of UniProt Q6N089
- Elsewhere: RCSB PDB 2OQJ · PDBe 2OQJ · UniProt Q6PIH4 · UniProt Q6N089
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