MolNFT v1 · #187370 · protein
Structure of the periplasmic domain of gldm from capnocytophaga canimorsus
7SB2: “Structure of the periplasmic domain of gldm from capnocytophaga canimorsus”. Electron microscopy, 8 pockets (best druggability 0.81). MolNFT v1 #187370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SB2
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gldm
- UniProt
- F9YQB7
- Pockets
- 8 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gldm | protein | 299 | 50% helix, 15% strand | F9YQB7 |
| B | Gldm | protein | 299 | 48% helix, 16% strand | F9YQB7 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.81 | 0.87 | 80 | empty |
| 2 | 421 | 0.73 | 0.83 | 48 | empty |
| 3 | 304 | 0.64 | 0.80 | 38 | empty |
| 4 | 72 | 0.56 | 0.88 | 23 | empty |
| 5 | 223 | 0.50 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 4138 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 7SB2 · Structure of the periplasmic domain of GldM from Capnocytophaga canimorsus · the same entry in another collection · chain B against B, 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 F9YQB7
- Elsewhere: RCSB PDB 7SB2 · PDBe 7SB2 · UniProt F9YQB7
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