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Structure of formate channel

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

PDB: 3KCU
Type: protein
Length: 1,240 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable formate transporter 1
UniProt: P0AC25
Ligands: MA5
Pockets: 19 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Probable formate transporter 1	protein	252	76% helix, 0% strand	P0AC25
C	Probable formate transporter 1	protein	239	78% helix, 0% strand	P0AC25
D	Probable formate transporter 1	protein	248	75% helix, 0% strand	P0AC25
E	Probable formate transporter 1	protein	249	74% helix, 0% strand	P0AC25

Ligands and binding sites

MA5 · 2-(6-(2-cyclohexylethoxy)-tetrahydro-4,5-dihydroxy-2(hydroxymethyl)-2H-pyran-3-yloxy)-tetrahydro-6(hydroxymethyl)-2H-py ran-3,4,5-triol · ligand · chains A

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

Pockets

19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1195	0.79	0.80	73	empty
2	277	0.66	0.81	28	empty
3	285	0.66	0.81	30	empty
4	286	0.66	0.81	28	empty
5	281	0.64	0.81	41	empty

Interfaces

5 interfaces between chains.

B–C · 1625 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1595 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 1505 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1501 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 1440 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3KCU · Structure of formate channel · the same entry in another collection · chain E against E, TM-score 1.00
P0AC25 · AlphaFold monomer V2.0 prediction for probable formate transporter 1 (P0AC25) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P0AC25
Elsewhere: RCSB PDB 3KCU · PDBe 3KCU · UniProt P0AC25

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