MolNFT v1 · #47031 · protein

Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)

2OME · C-terminal-binding protein 2: “Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.84). MolNFT v1 #47031 on GenesisL1: 3D structure, binding sites…

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.

Pocket	Volume (Å³)	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 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 3147 Å² buried · 43 hydrogen bonds · protein-protein
G–H · 3143 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 3129 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 997 Å² 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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