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Structure of caldicellulosiruptor danielii CBM3 module of glycoside hydrolase WP_045175321
Analyse Structure of caldicellulosiruptor danielii CBM3 module of glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D5B
- Type
- protein
- Length
- 1,835 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase WP_045175321
- EC
- 3.2.1.-
- Ligands
- CA
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, I, J, K, L | Glycoside hydrolase WP_045175321 (EC 3.2.1.-) | protein | 153 | 8% helix, 47% strand | — |
| B | Glycoside hydrolase WP_045175321 (EC 3.2.1.-) | protein | 154 | 6% helix, 46% strand | — |
| F, H | Glycoside hydrolase WP_045175321 (EC 3.2.1.-) | protein | 152 | 8% helix, 47% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.64 | 0.74 | 56 | empty |
| 2 | 549 | 0.61 | 0.74 | 47 | empty |
| 3 | 509 | 0.59 | 0.74 | 46 | empty |
| 4 | 412 | 0.58 | 0.75 | 44 | empty |
| 5 | 282 | 0.54 | 0.75 | 30 | empty |
Interfaces
18 interfaces between chains.
- E–F · 474 Ų buried · 14 hydrogen bonds · protein-protein
- G–L · 465 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 461 Ų buried · 12 hydrogen bonds · protein-protein
- J–K · 459 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6D5B · Structure of Caldicellulosiruptor danielii CBM3 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 6D5B · PDBe 6D5B
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