MolNFT v1 · #168582 · protein
EM structure of CTBP2 with a minimal dehydrogenase domain of CTBP2
6WKW · C-terminal-binding protein 2: “EM structure of CTBP2 with a minimal dehydrogenase domain of CTBP2”. Electron microscopy, 1 ligand (NAD), 12 pockets (best druggability 0.81). MolNFT v1 #168582 on GenesisL1: 3D structure, binding…
- PDB
- 6WKW
- Type
- protein
- Length
- 1,319 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-terminal-binding protein 2
- UniProt
- P56545
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 27% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | C-terminal-binding protein 2 | protein | 329 | 29% helix, 14% strand | P56545 |
| C, B, A | C-terminal-binding protein 2 | protein | 330 | 25% helix, 14% strand | P56545 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains D, C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.81 | 0.82 | 116 | NAD |
| 2 | 1084 | 0.81 | 0.82 | 121 | NAD |
| 3 | 721 | 0.74 | 0.80 | 56 | empty |
| 4 | 61 | 0.66 | 0.94 | 19 | empty |
| 5 | 143 | 0.51 | 0.80 | 29 | empty |
Interfaces
6 interfaces between chains.
- D–C · 3111 Ų buried · 36 hydrogen bonds · protein-protein
- B–A · 3010 Ų buried · 32 hydrogen bonds · protein-protein
- C–B · 959 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 917 Ų buried · 14 hydrogen bonds · protein-protein
- D–B · 177 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6WKW · EM structure of CtBP2 with a minimal dehydrogenase domain of CtBP2 · the same entry in another collection · chain A against A, 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 D against A, TM-score 0.99
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 6WKW · PDBe 6WKW · UniProt P56545
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