MolNFT v1 · #143988 · protein

Crystal structure of enolase from E. COLI with a mixture of apo form, substrate, and product form

6BFZ: “Crystal structure of enolase from E. COLI with a mixture of apo form, substrate, and product form”. X-ray diffraction, 4 ligands (2PG, PEP, MG), 18 pockets (best druggability 0.83). MolNFT v1 #143988 on GenesisL1: 3D structure…

PDB: 6BFZ
Type: protein
Length: 2,622 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enolase
EC: 4.2.1.11
UniProt: B7MLA0
Ligands: 2PG, PEP, MG, SO4
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Enolase (EC 4.2.1.11)	protein	439	43% helix, 19% strand	B7MLA0
F	Enolase (EC 4.2.1.11)	protein	438	42% helix, 19% strand	B7MLA0
D	Enolase (EC 4.2.1.11)	protein	438	42% helix, 18% strand	B7MLA0
C	Enolase (EC 4.2.1.11)	protein	429	42% helix, 17% strand	B7MLA0

Ligands and binding sites

2PG · 2-phosphoglyceric acid · ligand · 4 copies · chains E, F, D, C
PEP · Phosphoenolpyruvate · ligand · chains E
MG · Magnesium ion · metal · 6 copies · chains A, B, E, F, D, C
SO4 · Sulfate ion · ion · 13 copies · chains A, B, E, F, D, C
GOL · Glycerol · additive · 3 copies · chains A, B, E, F, D, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains E, D

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

Pockets

18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.83	0.90	102	GOL
2	508	0.79	0.86	47	empty
3	304	0.76	0.88	39	empty
4	79	0.73	0.97	28	PEP, 2PG
5	409	0.73	0.84	50	2PG, SO4

Interfaces

15 interfaces between chains.

E–F · 1943 Å² buried · 41 hydrogen bonds · protein-protein
D–C · 1907 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 1887 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 599 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 593 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6BFZ · Crystal structure of enolase from E. coli with a mixture of apo form, substrate, and… · the same entry in another collection · chain C against C, TM-score 1.00
B7MLA0 · AlphaFold monomer V2.0 prediction for enolase (B7MLA0) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 B7MLA0
Elsewhere: RCSB PDB 6BFZ · PDBe 6BFZ · UniProt B7MLA0

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