MolNFT v1 · #184931 · protein

Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from methanocaldococcus jannaschii in complex with onb-SAM (2-nitro benzyme S-adenosyl-methionine)

7P84 · S-adenosylmethionine synthase: “Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from methanocaldococcus…”. X-ray diffraction, 3 ligands (3PO, EU9, MG), 10 pockets (best druggability 0.82). MolNFT v1…

PDB: 7P84
Type: protein
Length: 814 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S-adenosylmethionine synthase
EC: 2.5.1.6
UniProt: Q58605
Ligands: 3PO, EU9, MG
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	S-adenosylmethionine synthase (EC 2.5.1.6)	protein	406	36% helix, 28% strand	Q58605
C	S-adenosylmethionine synthase (EC 2.5.1.6)	protein	408	34% helix, 29% strand	Q58605

Ligands and binding sites

3PO · Triphosphate · ligand · 2 copies · chains A, C
EU9 · [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methyl-[(3R)-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-[(2-nitrophenyl)methyl]sulfanium · ligand · chains A, C
MG · Magnesium ion · metal · 3 copies · chains A, C

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

Pockets

10 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	543	0.82	0.88	72	MG, 3PO, EU9
2	412	0.82	0.90	50	empty
3	867	0.76	0.80	80	3PO, MG
4	61	0.70	0.97	27	empty
5	279	0.54	0.76	39	empty

Interfaces

1 interface between chains.

A–C · 2747 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

7P84 · Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from… · the same entry in another collection · chain A against A, TM-score 1.00
Q58605 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine synthase (Q58605) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q58605
Elsewhere: RCSB PDB 7P84 · PDBe 7P84 · UniProt Q58605

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