MolNFT v1 · #12893 · protein

Human tissue transglutaminase in GDP bound form

1KV3 · Protein-glutamine gamma-glutamyltransferase: “Human tissue transglutaminase in GDP bound form”. X-ray diffraction, 1 ligand (GDP), 20 pockets (best druggability 0.87). MolNFT v1 #12893 on GenesisL1: 3D structure, binding sites and…

PDB: 1KV3
Type: protein
Length: 3,906 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-glutamine gamma-glutamyltransferase
EC: 2.3.2.13
UniProt: P21980
Ligands: GDP
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13)	protein	651	16% helix, 39% strand	P21980

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.87	0.88	85	empty
2	1024	0.87	0.88	88	empty
3	962	0.86	0.87	86	empty
4	928	0.79	0.81	105	empty
5	618	0.79	0.84	59	empty

Interfaces

5 interfaces between chains.

D–E · 1322 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1262 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 1235 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 777 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 751 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1KV3 · Human tissue transglutaminase in GDP bound form · the same entry in another collection · chain C against C, TM-score 1.00
P21980 · AlphaFold monomer V2.0 prediction for protein-glutamine gamma- glutamyltransferase 2… · a predicted model of the same protein · chain A 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 1KV3 · PDBe 1KV3 · UniProt P21980

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