MolNFT v1 · #88780 · protein

Crystal structure of cyma from klebsiella oxytoca

4D5D: “Crystal structure of cyma from klebsiella oxytoca”. X-ray diffraction, 1 ligand (GLC), 11 pockets (best druggability 0.69). MolNFT v1 #88780 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4D5D
Type: protein
Length: 620 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyma
UniProt: Q48391
Ligands: GLC
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 77% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyma	protein	311	2% helix, 77% strand	Q48391
B	Cyma	protein	309	2% helix, 77% strand	Q48391

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 26 copies · chains A, B
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 20 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	540	0.69	0.78	53	C8E
2	1145	0.67	0.73	107	empty
3	195	0.48	0.75	24	empty
4	106	0.42	0.78	19	empty
5	110	0.38	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1051 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4D5D · Crystal structure of CymA from Klebsiella oxytoca · 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 Q48391
Elsewhere: RCSB PDB 4D5D · PDBe 4D5D · UniProt Q48391

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