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Crystal structure of carbohydrate transporter MSMEG_3599 from mycobacterium smegmatis str. MC2 155, target efi-510970, in complex with D-threitol

Analyse Crystal structure of carbohydrate transporter MSMEG_3599 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RSM
Type: protein
Length: 1,257 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic binding PROTEIN/LACI transcriptional regulator
UniProt: A0QYB5
Ligands: 3VB
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Periplasmic binding PROTEIN/LACI transcriptional regulator	protein	315	49% helix, 18% strand	A0QYB5
C	Periplasmic binding PROTEIN/LACI transcriptional regulator	protein	314	49% helix, 18% strand	A0QYB5
D	Periplasmic binding PROTEIN/LACI transcriptional regulator	protein	313	48% helix, 18% strand	A0QYB5

Ligands and binding sites

3VB · D-Threitol · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1159	0.82	0.83	101	empty
2	1082	0.71	0.75	85	empty
3	199	0.51	0.77	37	empty
4	200	0.48	0.75	30	empty
5	144	0.41	0.75	25	empty

Interfaces

4 interfaces between chains.

A–D · 1100 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 774 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 702 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 126 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4RSM · Crystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis… · the same entry in another collection · chain A against A, TM-score 1.00
A0QYB5 · AlphaFold monomer V2.0 prediction for D-threitol-binding protein (A0QYB5) · a predicted model of the same protein · chain D against A, TM-score 1.00

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 A0QYB5
Elsewhere: RCSB PDB 4RSM · PDBe 4RSM · UniProt A0QYB5

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