Research workbench
Crystal structure of cbs domain, NE2398
Analyse Crystal structure of cbs domain, NE2398 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RC3
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cbs domain
- UniProt
- Q82SE2
- Ligands
- NAD, BR
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cbs domain | protein | 127 | 44% helix, 27% strand | Q82SE2 |
| B | Cbs domain | protein | 127 | 42% helix, 27% strand | Q82SE2 |
| C | Cbs domain | protein | 128 | 44% helix, 27% strand | Q82SE2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, B, C
- BR · Bromide ion · ion · 39 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.78 | 0.79 | 99 | BR, NAD |
| 2 | 475 | 0.71 | 0.81 | 49 | BR, NAD |
| 3 | 438 | 0.70 | 0.81 | 45 | BR, NAD |
| 4 | 378 | 0.69 | 0.82 | 41 | NAD, BR |
| 5 | 89 | 0.42 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1311 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1267 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 734 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2RC3 · Crystal structure of CBS domain, NE2398 · 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 Q82SE2
- Elsewhere: RCSB PDB 2RC3 · PDBe 2RC3 · UniProt Q82SE2
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