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Crystal Structure of human Enolase 1

Analyse Crystal Structure of human Enolase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B97
Type: protein
Length: 1,728 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Homo sapiens
Molecule: Alpha-enolase
EC: 4.2.1.11
UniProt: P06733
Ligands: MG, SO4
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · resolution 2.2 · 3 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alpha-enolase (EC 4.2.1.11)	protein	432	44% helix, 17% strand	P06733
C	Alpha-enolase (EC 4.2.1.11)	protein	433	45% helix, 17% strand	P06733
D	Alpha-enolase (EC 4.2.1.11)	protein	431	44% helix, 17% strand	P06733

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.74	0.77	58	empty
2	1070	0.74	0.77	59	empty
3	520	0.68	0.79	77	empty
4	249	0.57	0.78	36	empty
5	225	0.56	0.79	34	empty

Interfaces

3 interfaces between chains.

C–D · 2129 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2074 Å² buried · 46 hydrogen bonds · protein-protein
B–D · 707 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3B97 · Crystal structure of human enolase 1 · the same entry in another collection · chain D against D, TM-score 1.00
P06733 · AlphaFold monomer V2.0 prediction for alpha-enolase (P06733) · a predicted model of the same protein · chain D 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 P06733
Elsewhere: RCSB PDB 3B97 · PDBe 3B97 · UniProt P06733

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