MolNFT v1 · #155177 · protein

TRANSGLUTAMINASE2 complexed with calcium

6KZB · Protein-glutamine gamma-glutamyltransferase 2: “TRANSGLUTAMINASE2 complexed with calcium”. X-ray diffraction, 2 ligands (GDP, CA), 19 pockets (best druggability 0.85). MolNFT v1 #155177 on GenesisL1: 3D structure, binding sites and…

PDB: 6KZB
Type: protein
Length: 2,006 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-glutamine gamma-glutamyltransferase 2
EC: 2.3.2.13
UniProt: P21980
Ligands: GDP, CA
Pockets: 19 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13)	protein	681	15% helix, 40% strand	P21980
B	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13)	protein	676	16% helix, 39% strand	P21980
C	Protein-glutamine gamma-glutamyltransferase 2 (EC 2.3.2.13)	protein	649	16% helix, 39% strand	P21980

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
CA · Calcium ion · metal · 6 copies · chains A, B, C

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1042	0.85	0.86	97	empty
2	66	0.67	0.94	23	empty
3	218	0.63	0.82	40	empty
4	121	0.57	0.84	33	empty
5	308	0.57	0.76	33	empty

Interfaces

2 interfaces between chains.

B–C · 1207 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 141 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 3 disulfide (covalent ligand, disulfide).

Compared structures

6KZB · Transglutaminase2 complexed with calcium · the same entry in another collection · chain A against A, TM-score 1.00
P21980 · AlphaFold monomer V2.0 prediction for protein-glutamine gamma- glutamyltransferase 2… · a predicted model of the same protein · chain C 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 P21980
Elsewhere: RCSB PDB 6KZB · PDBe 6KZB · UniProt P21980

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