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Crystal structure of the fucose mutarotase in complex with L-fucose from streptococcus pneumoniae

Analyse Crystal structure of the fucose mutarotase in complex with L-fucose from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4A34
Type: protein
Length: 2,801 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RBSD/FUCU transport protein family protein
UniProt: Q04I09
Ligands: FUL, K
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H, J, K, L, M, N, O, P, Q, R, S, T	RBSD/FUCU transport protein family protein	protein	140	32% helix, 20% strand	Q04I09
E	RBSD/FUCU transport protein family protein	protein	139	33% helix, 20% strand	Q04I09
I	RBSD/FUCU transport protein family protein	protein	142	32% helix, 20% strand	Q04I09

Ligands and binding sites

FUL · beta-L-fucopyranose · sugar · 20 copies · chains A, E, B, C, D, F, G, H, I, J, K, O, L, M, N, P, Q, R, S, T
K · Potassium ion · metal · 10 copies · chains B, F, C, G, D, H, E, I, A, J, K, T, L, P, N, R, M, Q, O, S

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.77	0.80	96	K
2	559	0.74	0.82	77	K
3	494	0.74	0.83	75	K
4	169	0.74	0.91	30	empty
5	123	0.71	0.92	33	empty

Interfaces

42 interfaces between chains.

L–Q · 1004 Å² buried · 6 hydrogen bonds · protein-protein
D–I · 1001 Å² buried · 7 hydrogen bonds · protein-protein
N–S · 994 Å² buried · 9 hydrogen bonds · protein-protein
M–R · 986 Å² buried · 3 hydrogen bonds · protein-protein
C–H · 973 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4A34 · Crystal structure of the fucose mutarotase in complex with L-fucose from Streptococcus… · the same entry in another collection · chain A 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 Q04I09
Elsewhere: RCSB PDB 4A34 · PDBe 4A34 · UniProt Q04I09

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