MolNFT v1 · #10805 · protein

Crystal structure of escherichia COLI gene product yecd at 1.3 a resolution

1J2R · Hypothetical isochorismatase family protein yecd: “Crystal structure of escherichia COLI gene product yecd at 1.3 a resolution”. X-ray diffraction, 10 pockets (best druggability 0.87). MolNFT v1 #10805 on GenesisL1: 3D structure…

PDB: 1J2R
Type: protein
Length: 748 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical isochorismatase family protein yecd
UniProt: P37347
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Hypothetical isochorismatase family protein yecd	protein	188	35% helix, 21% strand	P37347
B	Hypothetical isochorismatase family protein yecd	protein	185	35% helix, 21% strand	P37347
C	Hypothetical isochorismatase family protein yecd	protein	187	35% helix, 21% strand	P37347

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	712	0.87	0.91	44	empty
2	383	0.71	0.82	36	MPD
3	355	0.71	0.83	40	MPD
4	378	0.70	0.82	36	MPD
5	380	0.70	0.82	41	MPD

Interfaces

6 interfaces between chains.

C–D · 1894 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1832 Å² buried · 31 hydrogen bonds · protein-protein
B–D · 760 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 746 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 162 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1J2R · Crystal structure of Escherichia coli gene product Yecd at 1.3 A resolution · 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 P37347
Elsewhere: RCSB PDB 1J2R · PDBe 1J2R · UniProt P37347

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