MolNFT v1 · #154919 · protein

Crystal structure of GH136 lacto-N-biosidase from eubacterium ramulus - native protein

6KQT: “Crystal structure of GH136 lacto-N-biosidase from eubacterium ramulus - native protein”. X-ray diffraction, 3 ligands (NAG, GAL, NA), 6 pockets (best druggability 0.61). MolNFT v1 #154919 on GenesisL1: 3D structure, binding sites…

PDB: 6KQT
Type: protein
Length: 619 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lacto-N-biosidase
UniProt: U2PDT9
Ligands: NAG, GAL, NA
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lacto-N-biosidase	protein	619	25% helix, 30% strand	U2PDT9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GAL · beta-D-galactopyranose · sugar · chains A
NA · Sodium ion · metal · chains A
PGE · Triethylene glycol · additive · chains A

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

Pockets

6 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	308	0.61	0.79	37	empty
2	289	0.60	0.79	38	NAG, GAL
3	429	0.60	0.75	42	empty
4	308	0.54	0.74	36	PGE
5	88	0.37	0.76	21	empty

Compared structures

6KQT · Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus - native protein · 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 U2PDT9
Elsewhere: RCSB PDB 6KQT · PDBe 6KQT · UniProt U2PDT9

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