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X-ray structures of cellulomonas parahominis L-ribose isomerase with no ligand

Analyse X-ray structures of cellulomonas parahominis L-ribose isomerase with no ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WW3
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-ribose isomerase
UniProt: L0N3Y0
Ligands: MN
Pockets: 7 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-ribose isomerase	protein	240	20% helix, 29% strand	L0N3Y0
B	L-ribose isomerase	protein	242	19% helix, 29% strand	L0N3Y0

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B

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

Pockets

7 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	51	0.66	0.96	20	empty
2	210	0.62	0.82	46	empty
3	260	0.58	0.78	32	empty
4	67	0.35	0.77	20	empty
5	85	0.33	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 2329 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

3WW3 · X-ray structures of Cellulomonas parahominis L-ribose isomerase with no ligand · the same entry in another collection · chain B against B, 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 L0N3Y0
Elsewhere: RCSB PDB 3WW3 · PDBe 3WW3 · UniProt L0N3Y0

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