MolNFT v1 · #160033 · protein
Crystal structure of antibody P-P1F1 in complex with eod-GT8
6P8N · Env outer domain eod-GT8: “Crystal structure of antibody P-P1F1 in complex with eod-GT8”. X-ray diffraction, 2 ligands (NAG, NH4), 14 pockets (best druggability 0.79). MolNFT v1 #160033 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6P8N
- Type
- protein
- Length
- 1,183 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Env outer domain eod-GT8; P-P1F1 heavy chain; P-P1F1 light chain
- Ligands
- NAG, NH4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Env outer domain eod-GT8 | protein | 167 | 17% helix, 31% strand | — |
| H | P-P1F1 heavy chain | protein | 221 | 4% helix, 48% strand | — |
| L | P-P1F1 light chain | protein | 204 | 7% helix, 50% strand | — |
| A | Env outer domain eod-GT8 | protein | 168 | 14% helix, 30% strand | — |
| B | P-P1F1 heavy chain | protein | 220 | 7% helix, 48% strand | — |
| D | P-P1F1 light chain | protein | 203 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- NH4 · Ammonium ion · ion · 3 copies · chains C, H, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.79 | 0.94 | 34 | empty |
| 2 | 140 | 0.77 | 0.94 | 26 | empty |
| 3 | 107 | 0.73 | 0.94 | 32 | empty |
| 4 | 52 | 0.67 | 0.96 | 18 | empty |
| 5 | 579 | 0.62 | 0.74 | 73 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1752 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1730 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 758 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 753 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 282 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6P8N · Crystal Structure of Antibody P-p1f1 in Complex with eOD-GT8 · the same entry in another collection · chain C against C, 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 6P8N · PDBe 6P8N
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