Research workbench

CCDBVFI:GYRA14EC

Analyse CCDBVFI:GYRA14EC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ELY
Type: protein
Length: 464 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA gyrase subunit a; Ccdb
EC: 5.99.1.3
UniProt: P0AES5, Q84B82
Ligands: CL, SO4
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA gyrase subunit a (EC 5.99.1.3)	protein	134	63% helix, 7% strand	P0AES5
C, D	Ccdb	protein	98	30% helix, 35% strand	Q84B82

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, D
SO4 · Sulfate ion · ion · chains A

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

Pockets

7 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	148	0.62	0.85	27	empty
2	358	0.60	0.76	43	empty
3	164	0.58	0.82	27	empty
4	263	0.55	0.76	39	empty
5	60	0.51	0.86	20	empty

Interfaces

6 interfaces between chains.

A–B · 1123 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 976 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 386 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 356 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 333 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4ELY · CCDBVFI:GYRA14EC · the same entry in another collection · chain A against A, TM-score 1.00
P0AES5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P0AES5) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0AES5
Every structure of UniProt Q84B82
Elsewhere: RCSB PDB 4ELY · PDBe 4ELY · UniProt P0AES5 · UniProt Q84B82

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