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Tric at 0.2 mm ADP-alfx, conformation 1, 0.2-C1

Analyse Tric at 0.2 mm ADP-alfx, conformation 1, 0.2-C1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KS6
Type: protein
Length: 8,502 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-complex protein 1 subunit alpha; T-complex protein 1 subunit beta; T-complex protein 1…
UniProt: P12612, P39076, P39078, P40413, P39077, P42943, P47079, P39079
Ligands: ADP, AF3, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 14 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	T-complex protein 1 subunit alpha	protein	546	47% helix, 17% strand	P12612
A	T-complex protein 1 subunit alpha	protein	550	45% helix, 14% strand	P12612
b, B	T-complex protein 1 subunit beta	protein	518	48% helix, 16% strand	P39076
d	T-complex protein 1 subunit delta	protein	524	47% helix, 17% strand	P39078
D	T-complex protein 1 subunit delta	protein	523	46% helix, 17% strand	P39078
e	T-complex protein 1 subunit epsilon	protein	535	50% helix, 13% strand	P40413
E	T-complex protein 1 subunit epsilon	protein	536	49% helix, 13% strand	P40413
g	Fusion protein of T-complex protein 1 subunit GAMMA,REP- his-cbp and T-complex protein 1 subunit gamma	protein	520	49% helix, 14% strand	P39077
G	Fusion protein of T-complex protein 1 subunit GAMMA,REP- his-cbp and T-complex protein 1 subunit gamma	protein	520	49% helix, 13% strand	P39077
h	T-complex protein 1 subunit eta	protein	527	48% helix, 14% strand	P42943
H	T-complex protein 1 subunit eta	protein	520	46% helix, 12% strand	P42943
q	T-complex protein 1 subunit theta	protein	541	45% helix, 12% strand	P47079
Q	T-complex protein 1 subunit theta	protein	548	46% helix, 12% strand	P47079
z, Z	T-complex protein 1 subunit zeta	protein	538	47% helix, 16% strand	P39079

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 16 copies · chains a, A, b, B, d, D, e, E, g, G, h, H, q, Q, z, Z
AF3 · Aluminum fluoride · ligand · 14 copies · chains a, A, b, B, d, D, e, E, g, G, h, H, z, Z
MG · Magnesium ion · metal · 16 copies · chains a, A, b, B, d, D, e, E, g, G, h, H, q, Q, z, Z

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	948	0.89	0.91	112	empty
2	1176	0.88	0.90	160	empty
3	846	0.86	0.89	93	ADP, MG, AF3
4	690	0.86	0.90	81	ADP, MG
5	835	0.85	0.87	82	MG, ADP

Interfaces

58 interfaces between chains.

a–g · 3833 Å² buried · 55 hydrogen bonds · protein-protein
B–E · 3748 Å² buried · 45 hydrogen bonds · protein-protein
g–z · 3698 Å² buried · 42 hydrogen bonds · protein-protein
b–e · 3677 Å² buried · 43 hydrogen bonds · protein-protein
G–Z · 3661 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

6KS6 · TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1 · the same entry in another collection · chain h against h, 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 P12612
Every structure of UniProt P39076
Every structure of UniProt P39078
Every structure of UniProt P40413
Every structure of UniProt P39077
Every structure of UniProt P42943
Every structure of UniProt P47079
Every structure of UniProt P39079
Elsewhere: RCSB PDB 6KS6 · PDBe 6KS6 · UniProt P12612 · UniProt P39076 · UniProt P39078 · UniProt P40413 · UniProt P39077 · UniProt P42943 · UniProt P47079 · UniProt P39079

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