MolNFT v1 · #175513 · protein + DNA

Pseudomonas aeruginosa antitoxin higa with higba promoter

7CSY · Hth CRO/C1-type domain-containing protein: “Pseudomonas aeruginosa antitoxin higa with higba promoter”. X-ray diffraction, 1 ligand (DT), 7 pockets (best druggability 0.75). MolNFT v1 #175513 on GenesisL1: 3D structure, binding…

PDB: 7CSY
Type: protein + DNA
Length: 433 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hth CRO/C1-type domain-containing protein; DNA (28-mer); DNA (29-mer)
UniProt: Q9HVC1
Ligands: DT
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hth CRO/C1-type domain-containing protein	protein	92	68% helix, 0% strand	Q9HVC1
B	Hth CRO/C1-type domain-containing protein	protein	97	68% helix, 0% strand	Q9HVC1
C	Hth CRO/C1-type domain-containing protein	protein	92	73% helix, 0% strand	Q9HVC1
D	Hth CRO/C1-type domain-containing protein	protein	95	66% helix, 0% strand	Q9HVC1
E	DNA (28-mer)	dna	28	—	—
F	DNA (29-mer)	dna	29	—	—

Ligands and binding sites

DT · Thymidine-5'-monophosphate · ligand · chains E, F

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

Pockets

7 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	1052	0.75	0.78	63	empty
2	832	0.70	0.77	55	empty
3	113	0.39	0.76	15	empty
4	75	0.35	0.77	15	empty
5	61	0.28	0.73	15	empty

Interfaces

11 interfaces between chains.

A–B · 1497 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1479 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1170 Å² buried · 113 hydrogen bonds · nucleic-nucleic
C–F · 318 Å² buried · 8 hydrogen bonds · protein-nucleic
A–E · 315 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

7CSY · Pseudomonas aeruginosa antitoxin HigA with higBA promoter · the same entry in another collection · chain A 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 Q9HVC1
Elsewhere: RCSB PDB 7CSY · PDBe 7CSY · UniProt Q9HVC1

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