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Bhmt from rat liver

Analyse Bhmt from rat liver in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UMY
Type: protein
Length: 1,515 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Betaine--homocysteine S-methyltransferase 1
EC: 2.1.1.5
UniProt: O09171
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5)	protein	374	48% helix, 9% strand	O09171
B	Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5)	protein	380	46% helix, 9% strand	O09171
C	Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5)	protein	380	46% helix, 9% strand	O09171
D	Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5)	protein	381	46% helix, 9% strand	O09171

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.81	0.99	31	empty
2	117	0.79	0.98	23	empty
3	773	0.78	0.82	57	BME
4	771	0.78	0.82	52	empty
5	804	0.78	0.81	60	BME

Interfaces

6 interfaces between chains.

A–B · 3472 Å² buried · 58 hydrogen bonds · protein-protein
C–D · 3429 Å² buried · 61 hydrogen bonds · protein-protein
A–C · 1474 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 1388 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 418 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1UMY · BHMT from rat liver · the same entry in another collection · chain D against D, TM-score 1.00
O09171 · AlphaFold monomer V2.0 prediction for betaine--homocysteine S-methyltransferase 1 (O09171) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O09171
Elsewhere: RCSB PDB 1UMY · PDBe 1UMY · UniProt O09171

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