Research workbench
Complex between human CD27 and Fab fragments of antibodies M2177 and H2191
Analyse Complex between human CD27 and Fab fragments of antibodies M2177 and H2191 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TLK
- Type
- protein
- Length
- 1,858 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M2177 light chain; M2177 heavy chain; H2191 light chain; H2191 heavy chain; CD27 antigen
- UniProt
- P26842
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.64
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | M2177 light chain | protein | 215 | 6% helix, 53% strand | — |
| B | M2177 heavy chain | protein | 213 | 9% helix, 51% strand | — |
| C, G | H2191 light chain | protein | 215 | 6% helix, 53% strand | — |
| D | H2191 heavy chain | protein | 212 | 6% helix, 52% strand | — |
| F | M2177 heavy chain | protein | 212 | 3% helix, 46% strand | — |
| H | H2191 heavy chain | protein | 211 | 4% helix, 53% strand | — |
| X, Y | CD27 antigen | protein | 75 | 0% helix, 32% strand | P26842 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains X, Y, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.64 | 0.75 | 64 | empty |
| 2 | 610 | 0.64 | 0.75 | 52 | empty |
| 3 | 629 | 0.64 | 0.74 | 65 | empty |
| 4 | 372 | 0.60 | 0.77 | 48 | empty |
| 5 | 302 | 0.58 | 0.77 | 41 | empty |
Interfaces
16 interfaces between chains.
- E–F · 1760 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1760 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1748 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1746 Ų buried · 15 hydrogen bonds · protein-protein
- F–Y · 489 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 4 modified, 2 glycan (disulfide, cyclization, N-glycosylation).
Compared structures
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 P26842
- Elsewhere: RCSB PDB 5TLK · PDBe 5TLK · UniProt P26842
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