Research workbench
Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)
Analyse Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OME
- Type
- protein
- Length
- 2,640 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-terminal-binding protein 2
- UniProt
- P56545
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | C-terminal-binding protein 2 | protein | 330 | 36% helix, 17% strand | P56545 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.84 | 0.85 | 115 | NAD |
| 2 | 1166 | 0.83 | 0.84 | 128 | NAD |
| 3 | 1132 | 0.82 | 0.83 | 123 | NAD |
| 4 | 1107 | 0.81 | 0.83 | 125 | NAD |
| 5 | 775 | 0.79 | 0.83 | 68 | empty |
Interfaces
17 interfaces between chains.
- E–F · 3167 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3147 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 3143 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3129 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 997 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2OME · Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H) · the same entry in another collection · chain H against H, TM-score 1.00
- P56545 · AlphaFold monomer V2.0 prediction for C-terminal-binding protein 2 (P56545) · a predicted model of the same protein · chain F 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
- Every structure of UniProt P56545
- Elsewhere: RCSB PDB 2OME · PDBe 2OME · UniProt P56545
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