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Crystal structure of a putative isochorismatase from streptomyces avermitilis

Analyse Crystal structure of a putative isochorismatase from streptomyces avermitilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KL2
Type: protein
Length: 2,407 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative isochorismatase
UniProt: Q82NB5
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative isochorismatase	protein	203	44% helix, 18% strand	Q82NB5
B, C, D, G, K, L	Putative isochorismatase	protein	200	43% helix, 18% strand	Q82NB5
E	Putative isochorismatase	protein	204	44% helix, 18% strand	Q82NB5
F	Putative isochorismatase	protein	201	44% helix, 18% strand	Q82NB5
H, J	Putative isochorismatase	protein	200	45% helix, 18% strand	Q82NB5
I	Putative isochorismatase	protein	199	41% helix, 18% strand	Q82NB5

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains B, C, H, K

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.82	0.94	45	empty
2	309	0.82	0.93	46	SO4
3	268	0.82	0.94	43	empty
4	753	0.76	0.81	76	empty
5	444	0.67	0.79	45	empty

Interfaces

22 interfaces between chains.

G–H · 1289 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1246 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1244 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1244 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 1224 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

3KL2 · Crystal structure of a putative isochorismatase from Streptomyces avermitilis · 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 Q82NB5
Elsewhere: RCSB PDB 3KL2 · PDBe 3KL2 · UniProt Q82NB5

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