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Crystal structure of rhamnonate dehydratase from gibberella zeae complexed with mg

Analyse Crystal structure of rhamnonate dehydratase from gibberella zeae complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FXG
Type: protein
Length: 3,247 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhamnonate dehydratase
UniProt: Q4HYS5
Ligands: MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Rhamnonate dehydratase	protein	407	39% helix, 15% strand	Q4HYS5
B	Rhamnonate dehydratase	protein	406	39% helix, 15% strand	Q4HYS5
C, D, H	Rhamnonate dehydratase	protein	405	39% helix, 15% strand	Q4HYS5
F, G	Rhamnonate dehydratase	protein	406	39% helix, 16% strand	Q4HYS5

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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	204	0.83	0.96	34	empty
2	178	0.83	0.97	27	empty
3	1006	0.82	0.83	92	empty
4	166	0.82	0.97	23	empty
5	159	0.81	0.97	23	empty

Interfaces

16 interfaces between chains.

G–H · 2653 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2647 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2645 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 2629 Å² buried · 29 hydrogen bonds · protein-protein
B–E · 1843 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 modified (engineered).

Compared structures

3FXG · Crystal structure of rhamnonate dehydratase from Gibberella zeae complexed with Mg · 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 Q4HYS5
Elsewhere: RCSB PDB 3FXG · PDBe 3FXG · UniProt Q4HYS5

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