MolNFT v1 · #117811 · protein

The crystal structure of holo T3CT

5EJD · Tqaa: “The crystal structure of holo T3CT”. X-ray diffraction, 1 ligand (5PD), 20 pockets (best druggability 0.81). MolNFT v1 #117811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EJD
Type: protein
Length: 4,070 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tqaa
UniProt: F1CWE4
Ligands: 5PD
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 9 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, J, P	Tqaa	protein	436	33% helix, 24% strand	F1CWE4
A, G	Tqaa	protein	75	57% helix, 3% strand	F1CWE4
D	Tqaa	protein	437	33% helix, 24% strand	F1CWE4
C	Tqaa	protein	74	54% helix, 3% strand	F1CWE4
F, H, L, N	Tqaa	protein	435	33% helix, 24% strand	F1CWE4
E, I	Tqaa	protein	72	58% helix, 3% strand	F1CWE4
K	Tqaa	protein	73	53% helix, 3% strand	F1CWE4
M	Tqaa	protein	70	57% helix, 3% strand	F1CWE4
O	Tqaa	protein	74	58% helix, 3% strand	F1CWE4

Ligands and binding sites

5PD · (R)-3-hydroxy-4-((3-((2-mercaptoethyl)amino)-3-oxopropyl)amino)-2,2-dimethyl-4-oxobutyl hydrogen phosphonate · ligand · 8 copies · chains B, A, D, C, F, E, H, G, J, I, L, K, N, M, P, O
GOL · Glycerol · additive · 3 copies · chains B, D, P

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	1010	0.81	0.82	96	empty
2	1047	0.80	0.82	86	empty
3	871	0.79	0.82	81	empty
4	394	0.78	0.87	50	GOL, 5PD
5	398	0.77	0.86	46	GOL, 5PD

Interfaces

27 interfaces between chains.

D–F · 973 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 898 Å² buried · 10 hydrogen bonds · protein-protein
L–K · 740 Å² buried · 4 hydrogen bonds · protein-protein
N–M · 739 Å² buried · 2 hydrogen bonds · protein-protein
H–G · 716 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

5EJD · The crystal structure of holo T3CT · the same entry in another collection · chain B against B, 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 F1CWE4
Elsewhere: RCSB PDB 5EJD · PDBe 5EJD · UniProt F1CWE4

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