MolNFT v1 · #106685 · protein

Crystal structure of gyrase bound to its inhibitor yacg

4TMA · DNA gyrase subunit a: “Crystal structure of gyrase bound to its inhibitor yacg”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #106685 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4TMA
Type: protein
Length: 3,385 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA gyrase subunit a; DNA gyrase subunit B; DNA gyrase inhibitor yacg
EC: 5.99.1.3
UniProt: U6NB78, U6NGU8, P0A8H8
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 12 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA gyrase subunit a (EC 5.99.1.3)	protein	505	45% helix, 15% strand	U6NB78
B	DNA gyrase subunit B (EC 5.99.1.3)	protein	374	45% helix, 20% strand	U6NGU8
C	DNA gyrase subunit a (EC 5.99.1.3)	protein	475	48% helix, 13% strand	U6NB78
D	DNA gyrase subunit B (EC 5.99.1.3)	protein	251	49% helix, 15% strand	U6NGU8
E	DNA gyrase subunit a (EC 5.99.1.3)	protein	486	46% helix, 15% strand	U6NB78
F	DNA gyrase subunit B (EC 5.99.1.3)	protein	371	43% helix, 22% strand	U6NGU8
G	DNA gyrase subunit a (EC 5.99.1.3)	protein	483	44% helix, 15% strand	U6NB78
H	DNA gyrase subunit B (EC 5.99.1.3)	protein	233	46% helix, 16% strand	U6NGU8
I	DNA gyrase inhibitor yacg	protein	47	26% helix, 13% strand	P0A8H8
J	DNA gyrase inhibitor yacg	protein	57	21% helix, 14% strand	P0A8H8
K	DNA gyrase inhibitor yacg	protein	55	24% helix, 13% strand	P0A8H8
L	DNA gyrase inhibitor yacg	protein	48	25% helix, 13% strand	P0A8H8

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, E, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	830	0.81	0.84	106	ZN
2	1067	0.81	0.82	115	empty
3	680	0.75	0.81	64	empty
4	752	0.73	0.79	75	empty
5	477	0.73	0.82	46	empty

Interfaces

29 interfaces between chains.

A–C · 1795 Å² buried · 15 hydrogen bonds · protein-protein
E–G · 1744 Å² buried · 21 hydrogen bonds · protein-protein
F–G · 1320 Å² buried · 30 hydrogen bonds · protein-protein
E–H · 1269 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1266 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4TMA · Crystal structure of gyrase bound to its inhibitor YacG · the same entry in another collection · chain F against F, 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 U6NB78
Every structure of UniProt U6NGU8
Every structure of UniProt P0A8H8
Elsewhere: RCSB PDB 4TMA · PDBe 4TMA · UniProt U6NB78 · UniProt U6NGU8 · UniProt P0A8H8

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