MolNFT v1 · #30181 · protein + DNA

Crystal structure of a ccpa-crh-DNA complex

1ZVV · DNA recognition strand cre: “Crystal structure of a ccpa-crh-DNA complex”. X-ray diffraction, 1 ligand (IOD), 13 pockets (best druggability 0.68). MolNFT v1 #30181 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZVV
Type: protein + DNA
Length: 1,293 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA recognition strand cre; Glucose-resistance amylase regulator; Hpr-like protein crh
UniProt: P46828, O06976
Ligands: IOD
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O, T, R	DNA recognition strand cre	dna	16	—	—
A, B	Glucose-resistance amylase regulator	protein	332	44% helix, 13% strand	P46828
W, P, J	Hpr-like protein crh	protein	84	36% helix, 27% strand	O06976
G	Glucose-resistance amylase regulator	protein	329	40% helix, 14% strand	P46828

Ligands and binding sites

IOD · Iodide ion · ion · 11 copies · chains O, A, B, P, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.68	0.88	27	empty
2	390	0.67	0.80	47	empty
3	195	0.66	0.85	31	IOD
4	223	0.58	0.80	25	empty
5	197	0.51	0.77	27	empty

Interfaces

8 interfaces between chains.

B–P · 720 Å² buried · 8 hydrogen bonds · protein-protein
A–W · 698 Å² buried · 7 hydrogen bonds · protein-protein
G–J · 685 Å² buried · 8 hydrogen bonds · protein-protein
R–G · 477 Å² buried · 8 hydrogen bonds · protein-nucleic
T–B · 470 Å² buried · 12 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 modified (phosphorylation).

Compared structures

1ZVV · Crystal structure of a ccpa-crh-dna complex · the same entry in another collection · chain P against P, TM-score 1.00
P46828 · AlphaFold monomer V2.0 prediction for catabolite control protein a (P46828) · a predicted model of the same protein · chain B 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 P46828
Every structure of UniProt O06976
Elsewhere: RCSB PDB 1ZVV · PDBe 1ZVV · UniProt P46828 · UniProt O06976

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