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Structure of GAP31

Analyse Structure of GAP31 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KTZ
Type: protein
Length: 502 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome-inactivating protein gelonin
EC: 3.2.2.22
UniProt: P33186
Ligands: NAG
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribosome-inactivating protein gelonin (EC 3.2.2.22)	protein	251	37% helix, 24% strand	P33186

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	439	0.70	0.81	60	empty
2	180	0.43	0.73	30	empty
3	148	0.42	0.74	27	empty
4	58	0.32	0.77	14	empty
5	51	0.28	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 1011 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3KTZ · Structure of GAP31 · the same entry in another collection · chain A against A, TM-score 1.00
P33186 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein gelonin (P33186) · a predicted model of the same protein · 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 P33186
Elsewhere: RCSB PDB 3KTZ · PDBe 3KTZ · UniProt P33186

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