MolNFT v1 · #69400 · protein

Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L- methionine.

3KPD · Uncharacterized protein MJ0100: “Crystal structure of the cbs domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and…”. X-ray diffraction, 2 ligands (MTA, SAM), 8 pockets (best druggability 0.74). MolNFT v1 #69400…

PDB: 3KPD
Type: protein
Length: 478 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein MJ0100
UniProt: Q57564
Ligands: MTA, SAM
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Uncharacterized protein MJ0100	protein	119	31% helix, 26% strand	Q57564
B	Uncharacterized protein MJ0100	protein	121	36% helix, 25% strand	Q57564

Ligands and binding sites

MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 5 copies · chains A, C, D
SAM · S-adenosylmethionine · ligand · 2 copies · chains B, C

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	630	0.74	0.81	76	SAM, MTA
2	831	0.71	0.77	72	MTA
3	371	0.67	0.81	40	empty
4	199	0.60	0.82	29	empty
5	65	0.38	0.78	13	MTA

Interfaces

4 interfaces between chains.

B–C · 1533 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 698 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 596 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 110 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3KPD · Crystal Structure of the CBS domain pair of protein MJ0100 in complex with 5… · the same entry in another collection · chain D against D, TM-score 1.00
Q57564 · AlphaFold monomer V2.0 prediction for L-aspartate semialdehyde sulfurtransferase (Q57564) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q57564
Elsewhere: RCSB PDB 3KPD · PDBe 3KPD · UniProt Q57564

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