MolNFT v1 · #129483 · protein

Rhamnogalacturonan lyase

5OLS: “Rhamnogalacturonan lyase”. X-ray diffraction, 5 ligands (GTR, AQA, RAM), 2 pockets (best druggability 0.39). MolNFT v1 #129483 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OLS
Type: protein
Length: 425 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhamnogalacturonan lyase
UniProt: A0A139KMS2
Ligands: GTR, AQA, RAM, ADA, CA
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhamnogalacturonan lyase	protein	425	7% helix, 34% strand	A0A139KMS2

Ligands and binding sites

GTR · beta-D-galactopyranuronic acid · ligand · chains A
AQA · 4-deoxy-beta-L-threo-hex-4-enopyranuronic acid · ligand · chains A
RAM · alpha-L-rhamnopyranose · sugar · 3 copies · chains A
ADA · alpha-D-galactopyranuronic acid · sugar · chains A
CA · Calcium ion · metal · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	124	0.39	0.75	23	RAM, AQA
2	67	0.34	0.77	19	empty

Compared structures

5OLS · Rhamnogalacturonan lyase · 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 A0A139KMS2
Elsewhere: RCSB PDB 5OLS · PDBe 5OLS · UniProt A0A139KMS2

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