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Crystal structure of lige-apo form from sphingobium sp. strain syk-6

Analyse Crystal structure of lige-apo form from sphingobium sp. strain syk-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YAM
Type: protein
Length: 1,005 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-etherase
UniProt: P27457
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-etherase	protein	250	50% helix, 10% strand	P27457
B, C	Beta-etherase	protein	252	48% helix, 10% strand	P27457
D	Beta-etherase	protein	251	49% helix, 10% strand	P27457

Pockets

11 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	470	0.73	0.82	51	empty
2	274	0.58	0.78	28	empty
3	267	0.57	0.77	30	empty
4	266	0.56	0.77	28	empty
5	284	0.56	0.76	29	empty

Interfaces

4 interfaces between chains.

A–B · 1110 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1107 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 692 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

4YAM · Crystal structure of LigE-apo form from Sphingobium sp. strain SYK-6 · the same entry in another collection · chain A against A, TM-score 1.00
P27457 · AlphaFold monomer V2.0 prediction for beta-etherase (P27457) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P27457
Elsewhere: RCSB PDB 4YAM · PDBe 4YAM · UniProt P27457

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