MolNFT v1 · #55563 · protein

Crystal structure of pula from klebsiella oxytoca

2YOC · Pullulanase: “Crystal structure of pula from klebsiella oxytoca”. X-ray diffraction, 2 ligands (CA, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #55563 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YOC
Type: protein
Length: 2,106 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pullulanase
EC: 3.2.1.41
UniProt: P07206
Ligands: CA, SO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pullulanase (EC 3.2.1.41)	protein	1051	27% helix, 23% strand	P07206
B	Pullulanase (EC 3.2.1.41)	protein	1055	27% helix, 23% strand	P07206

Ligands and binding sites

CA · Calcium ion · metal · 8 copies · chains A, B
SO4 · Sulfate ion · ion · 14 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	831	0.78	0.81	86	empty
2	121	0.67	0.89	31	empty
3	353	0.66	0.80	51	empty
4	193	0.63	0.83	36	empty
5	381	0.61	0.77	38	SO4

Interfaces

1 interface between chains.

A–B · 1387 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 44 modified, 6 disulfide (engineered, disulfide).

Compared structures

2YOC · Crystal structure of PulA from Klebsiella oxytoca · the same entry in another collection · chain A against A, TM-score 1.00
P07206 · AlphaFold monomer V2.0 prediction for pullulanase (P07206) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P07206
Elsewhere: RCSB PDB 2YOC · PDBe 2YOC · UniProt P07206

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