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Crystal structure of a putative uncharacterized protein from mycobacterium marinum bound to adenosine 5'-monophosphate AMP

Analyse Crystal structure of a putative uncharacterized protein from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SBX
Type: protein
Length: 1,416 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein
UniProt: B2HS63
Ligands: AMP
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Putative uncharacterized protein	protein	177	45% helix, 19% strand	B2HS63

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	775	0.83	0.86	78	AMP
2	864	0.79	0.82	100	AMP
3	195	0.71	0.88	37	AMP
4	167	0.71	0.89	35	AMP
5	232	0.69	0.85	34	AMP

Interfaces

12 interfaces between chains.

A–B · 1783 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1748 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1734 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1712 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 610 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3SBX · Crystal structure of a putative uncharacterized protein from Mycobacterium marinum bound… · the same entry in another collection · chain H against H, TM-score 1.00
B2HS63 · AlphaFold monomer V2.0 prediction for cytokinin riboside 5'-monophosphate… · a predicted model of the same protein · chain A 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 B2HS63
Elsewhere: RCSB PDB 3SBX · PDBe 3SBX · UniProt B2HS63

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