MolNFT v1 · #57469 · protein

Crystal structure of et-ehred-5-CH3-thf complex

3A8I · Aminomethyltransferase: “Crystal structure of et-ehred-5-CH3-thf complex”. X-ray diffraction, 2 ligands (C2F, PO4), 15 pockets (best druggability 0.81). MolNFT v1 #57469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A8I
Type: protein
Length: 1,708 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminomethyltransferase; Glycine cleavage system H protein
EC: 2.1.2.10
UniProt: P27248, P0A6T9
Ligands: C2F, PO4
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aminomethyltransferase (EC 2.1.2.10)	protein	363	26% helix, 35% strand	P27248
E, F	Glycine cleavage system H protein	protein	128	21% helix, 34% strand	P0A6T9

Ligands and binding sites

C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 4 copies · chains A, E, B, F, C, D
PO4 · Phosphate ion · ion · 2 copies · chains C, D

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.81	0.82	104	C2F
2	314	0.68	0.82	46	C2F
3	290	0.66	0.82	35	C2F
4	317	0.65	0.81	47	C2F
5	56	0.52	0.88	21	empty

Interfaces

6 interfaces between chains.

B–D · 955 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 946 Å² buried · 20 hydrogen bonds · protein-protein
B–F · 895 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 887 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 324 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3A8I · Crystal Structure of ET-EHred-5-CH3-THF complex · the same entry in another collection · chain B against B, TM-score 1.00
P27248 · AlphaFold monomer V2.0 prediction for aminomethyltransferase (P27248) · a predicted model of the same protein · chain C against A, TM-score 0.99
P0A6T9 · AlphaFold monomer V2.0 prediction for glycine cleavage system H protein (P0A6T9) · a predicted model of the same protein · chain F against A, TM-score 0.96

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 P27248
Every structure of UniProt P0A6T9
Elsewhere: RCSB PDB 3A8I · PDBe 3A8I · UniProt P27248 · UniProt P0A6T9

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