MolNFT v1 · #57470 · protein

Crystal structure of et-ehred complex

3A8J · Aminomethyltransferase: “Crystal structure of et-ehred complex”. X-ray diffraction, 13 pockets (best druggability 0.82). MolNFT v1 #57470 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3A8J
Type: protein
Length: 1,707 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
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 3 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, 36% strand	P27248
E	Glycine cleavage system H protein	protein	127	24% helix, 34% strand	P0A6T9
F	Glycine cleavage system H protein	protein	128	24% helix, 34% strand	P0A6T9

Pockets

13 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	1170	0.82	0.83	137	empty
2	467	0.75	0.83	68	empty
3	406	0.73	0.83	55	empty
4	457	0.72	0.82	64	empty
5	110	0.50	0.82	28	empty

Interfaces

6 interfaces between chains.

B–D · 975 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 960 Å² buried · 21 hydrogen bonds · protein-protein
B–F · 867 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 836 Å² buried · 13 hydrogen bonds · protein-protein
B–E · 349 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

3A8J · Crystal Structure of ET-EHred complex · the same entry in another collection · chain F against F, 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 E 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 P27248
Every structure of UniProt P0A6T9
Elsewhere: RCSB PDB 3A8J · PDBe 3A8J · UniProt P27248 · UniProt P0A6T9

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