Research workbench
Structure of FAB4 bound to P22 TERL(1-33)
Analyse Structure of FAB4 bound to P22 TERL(1-33) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VI1
- Type
- protein
- Length
- 2,808 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic FAB4 light chain; Synthetic FAB4 heavy chain; Terminase, large subunit
- EC
- 3.1.21.4, 3.6.4.12, 3.6.4.-
- UniProt
- P26745
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, C, G, I, K | Synthetic FAB4 light chain | protein | 214 | 7% helix, 52% strand | — |
| E, J | Synthetic FAB4 heavy chain | protein | 230 | 7% helix, 52% strand | — |
| B, L | Synthetic FAB4 heavy chain | protein | 232 | 8% helix, 52% strand | — |
| F, H | Synthetic FAB4 heavy chain | protein | 231 | 5% helix, 52% strand | — |
| M, N, O, P, Q, R | Terminase, large subunit (EC 3.1.21.4, 3.6.4.12, 3.6.4.-) | protein | 23 | 61% helix, 4% strand | P26745 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.71 | 0.75 | 103 | empty |
| 2 | 749 | 0.68 | 0.76 | 63 | empty |
| 3 | 666 | 0.63 | 0.74 | 67 | empty |
| 4 | 590 | 0.62 | 0.74 | 58 | empty |
| 5 | 577 | 0.62 | 0.74 | 58 | empty |
Interfaces
31 interfaces between chains.
- A–B · 2142 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2117 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 2085 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1972 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 1950 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 6VI1 · Structure of Fab4 bound to P22 TerL(1-33) · the same entry in another collection · chain D against D, 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 P26745
- Elsewhere: RCSB PDB 6VI1 · PDBe 6VI1 · UniProt P26745
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