MolNFT v1 · #154178 · protein + DNA

Crystal structure of the DNA complex of C. crescentus gapr

6K2J · UPF0335 protein CCNA_03428: “Crystal structure of the DNA complex of C. crescentus gapr”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #154178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6K2J
Type: protein + DNA
Length: 358 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0335 protein CCNA_03428; 10A DNA_FRONT; 10A DNA_REVERSE
UniProt: B8H4R9
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0335 protein CCNA_03428	protein	80	89% helix, 0% strand	B8H4R9
B, D	UPF0335 protein CCNA_03428	protein	83	93% helix, 0% strand	B8H4R9
C	UPF0335 protein CCNA_03428	protein	82	89% helix, 0% strand	B8H4R9
E	10A DNA_FRONT	dna	15	—	—
F	10A DNA_REVERSE	dna	15	—	—

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.77	0.83	57	empty
2	931	0.77	0.80	59	empty

Interfaces

12 interfaces between chains.

C–D · 1408 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1372 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 748 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 685 Å² buried · 58 hydrogen bonds · nucleic-nucleic
B–E · 276 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6K2J · Crystal Structure of the DNA Complex of C. crescentus GapR · the same entry in another collection · chain F against F, TM-score 1.00
B8H4R9 · AlphaFold monomer V2.0 prediction for UPF0335 protein CCNA_03428 (B8H4R9) · a predicted model of the same protein · chain A against A, TM-score 0.68

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 B8H4R9
Elsewhere: RCSB PDB 6K2J · PDBe 6K2J · UniProt B8H4R9

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