Research workbench
Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 4E10 fv complex
Analyse Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 4E10 fv complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LH2
- Type
- protein
- Length
- 1,210 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10_1VI7A_S0_002_N (T88); Fv 4E10 heavy chain; Fv 4E10 light chain
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 9 distinct chains · 13% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | 4E10_1VI7A_S0_002_N (T88) | protein | 64 | 34% helix, 39% strand | — |
| H | Fv 4E10 heavy chain | protein | 127 | 5% helix, 53% strand | — |
| T | 4E10_1VI7A_S0_002_N (T88) | protein | 67 | 42% helix, 39% strand | — |
| I | Fv 4E10 heavy chain | protein | 127 | 8% helix, 53% strand | — |
| V, U | 4E10_1VI7A_S0_002_N (T88) | protein | 68 | 38% helix, 38% strand | — |
| K | Fv 4E10 heavy chain | protein | 126 | 5% helix, 54% strand | — |
| L, O, N | Fv 4E10 light chain | protein | 110 | 5% helix, 47% strand | — |
| M | Fv 4E10 light chain | protein | 108 | 6% helix, 48% strand | — |
| J | Fv 4E10 heavy chain | protein | 125 | 5% helix, 54% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.71 | 0.78 | 74 | empty |
| 2 | 559 | 0.71 | 0.80 | 54 | empty |
| 3 | 748 | 0.68 | 0.75 | 62 | empty |
| 4 | 675 | 0.66 | 0.75 | 61 | empty |
| 5 | 481 | 0.63 | 0.76 | 57 | empty |
Interfaces
25 interfaces between chains.
- T–U · 3033 Ų buried · 61 hydrogen bonds · protein-protein
- S–V · 2933 Ų buried · 52 hydrogen bonds · protein-protein
- K–O · 790 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 744 Ų buried · 8 hydrogen bonds · protein-protein
- N–J · 734 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3LH2 · Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 4E10 Fv complex · the same entry in another collection · chain S against S, 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
- Elsewhere: RCSB PDB 3LH2 · PDBe 3LH2
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