MolNFT v1 · #146027 · protein
Structure of caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321
6D5C: “Structure of caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.72). MolNFT v1 #146027 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D5C
- Type
- protein
- Length
- 1,011 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase WP_045175321
- EC
- 3.2.1.-
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glycoside hydrolase WP_045175321 (EC 3.2.1.-) | protein | 337 | 41% helix, 20% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.72 | 0.80 | 63 | EDO, GOL |
| 2 | 421 | 0.68 | 0.80 | 53 | SO4, EDO, GOL |
| 3 | 286 | 0.62 | 0.79 | 39 | EDO |
| 4 | 211 | 0.50 | 0.76 | 32 | SO4 |
| 5 | 80 | 0.40 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 713 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6D5C · Structure of Caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321 · the same entry in another collection · chain A against A, 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 6D5C · PDBe 6D5C
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.