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Crystal structure of E. COLI se-met protein ydde

Analyse Crystal structure of E. COLI se-met protein ydde in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QY9
Type: protein
Length: 1,183 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ydde
UniProt: P37757
Ligands: OH
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hypothetical protein ydde	protein	295	24% helix, 40% strand	P37757
C	Hypothetical protein ydde	protein	296	24% helix, 40% strand	P37757
D	Hypothetical protein ydde	protein	297	24% helix, 40% strand	P37757

Ligands and binding sites

OH · Hydroxide ion · ion · chains B
GOL · Glycerol · additive · 3 copies · chains A, D

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

Pockets

12 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	457	0.73	0.83	61	GOL
2	1038	0.73	0.76	93	GOL
3	631	0.67	0.76	57	empty
4	252	0.63	0.82	35	OH
5	206	0.63	0.83	36	GOL

Interfaces

4 interfaces between chains.

A–B · 1061 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1050 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 524 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 87 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified, 2 covalent (engineered, additive adduct).

Compared structures

1QY9 · Crystal structure of E. coli Se-MET protein YDDE · the same entry in another collection · chain A against A, TM-score 1.00
P37757 · AlphaFold monomer V2.0 prediction for uncharacterized isomerase ydde (P37757) · a predicted model of the same protein · 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 P37757
Elsewhere: RCSB PDB 1QY9 · PDBe 1QY9 · UniProt P37757

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