MolNFT v1 · #98864 · protein

Crystal structure of the jcv large T-antigen origin binding domain

4LMD · Large T antigen: “Crystal structure of the jcv large T-antigen origin binding domain”. X-ray diffraction, 3 pockets (best druggability 0.43). MolNFT v1 #98864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4LMD
Type: protein
Length: 258 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Large T antigen
EC: 3.6.4.-
UniProt: P03072
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Large T antigen (EC 3.6.4.-)	protein	128	31% helix, 31% strand	P03072
B	Large T antigen (EC 3.6.4.-)	protein	130	33% helix, 30% strand	P03072

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B
FLC · Citrate anion · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.43	0.80	19	GOL
2	81	0.37	0.76	14	empty
3	90	0.32	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 565 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4LMD · Crystal structure of the JCV large t-antigen origin binding domain · 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 P03072
Elsewhere: RCSB PDB 4LMD · PDBe 4LMD · UniProt P03072

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