MolNFT v1 · #144678 · protein

Crystal structure of efga from methylobacterium extorquens in complex with formaldehyde

6C0Z: “Crystal structure of efga from methylobacterium extorquens in complex with formaldehyde”. X-ray diffraction, 1 ligand (21H), 3 pockets (best druggability 0.75). MolNFT v1 #144678 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6C0Z
Type: protein
Length: 548 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Efga
UniProt: H1KGY6
Ligands: 21H
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, D	Efga	protein	137	39% helix, 19% strand	H1KGY6

Ligands and binding sites

21H · oxydimethanol · ligand · 3 copies · chains A, D, C
FMT · Formic acid · additive · chains B, C

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.75	0.78	55	empty
2	238	0.54	0.77	30	empty
3	189	0.54	0.79	27	empty

Interfaces

5 interfaces between chains.

B–A · 835 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 689 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 683 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 198 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 188 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6C0Z · Crystal structure of Efga from Methylobacterium extorquens in complex with formaldehyde · the same entry in another collection · chain B against B, 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 H1KGY6
Elsewhere: RCSB PDB 6C0Z · PDBe 6C0Z · UniProt H1KGY6

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