MolNFT v1 · #176488 · protein
Crystal structure of gd-26 Fab in complex with td peptide from haloarcula marismortui bacteriorhodopsin I
7DOH · Gly-thr-gly-ala-thr-pro-ala-asp-asp: “Crystal structure of gd-26 Fab in complex with td peptide from haloarcula marismortui bacteriorhodopsin I”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #176488 on GenesisL1…
- PDB
- 7DOH
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gly-thr-gly-ala-thr-pro-ala-asp-asp; Gd-26 Fab L-chain; Gd-26 Fab H-chain
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Gly-thr-gly-ala-thr-pro-ala-asp-asp | protein | 9 | 33% helix, 0% strand | — |
| L | Gd-26 Fab L-chain | protein | 218 | 6% helix, 51% strand | — |
| H | Gd-26 Fab H-chain | protein | 210 | 9% helix, 54% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.55 | 0.74 | 46 | empty |
| 2 | 84 | 0.36 | 0.75 | 22 | empty |
| 3 | 76 | 0.29 | 0.73 | 17 | empty |
| 4 | 54 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1668 Ų buried · 16 hydrogen bonds · protein-protein
- I–L · 312 Ų buried · 6 hydrogen bonds · protein-protein
- I–H · 222 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DOH · Crystal Structure of GD-26 Fab in Complex with TD Peptide from Haloarcula Marismortui… · the same entry in another collection · chain L against L, 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 7DOH · PDBe 7DOH
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