Research workbench

Human tric complex in closed state with nanobody and tubulin bound

Analyse Human tric complex in closed state with nanobody and tubulin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NVN
Type: protein
Length: 8,970 residues
Chains: 19
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: P17987, P78371, P50991, P48643, P49368, Q99832, P50990, P40227, Q13885
Ligands: ADP, AF3, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 16 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-complex protein 1 subunit alpha	protein	535	52% helix, 19% strand	P17987
B	T-complex protein 1 subunit beta	protein	526	51% helix, 18% strand	P78371
D, d	T-complex protein 1 subunit delta	protein	519	50% helix, 18% strand	P50991
E	T-complex protein 1 subunit epsilon	protein	537	49% helix, 18% strand	P48643
G, g	T-complex protein 1 subunit gamma	protein	523	50% helix, 16% strand	P49368
H, h	T-complex protein 1 subunit eta	protein	524	48% helix, 18% strand	Q99832
N	Nanobody	protein	109	6% helix, 53% strand	—
Q	T-complex protein 1 subunit theta	protein	530	50% helix, 18% strand	P50990
Z	T-complex protein 1 subunit zeta	protein	529	53% helix, 17% strand	P40227
a	T-complex protein 1 subunit alpha	protein	536	51% helix, 19% strand	P17987
b	T-complex protein 1 subunit beta	protein	527	51% helix, 18% strand	P78371
e	T-complex protein 1 subunit epsilon	protein	538	49% helix, 18% strand	P48643
n	Nanobody	protein	109	3% helix, 50% strand	—
q	T-complex protein 1 subunit theta	protein	529	50% helix, 18% strand	P50990
z	T-complex protein 1 subunit zeta	protein	526	53% helix, 17% strand	P40227
T	Tubulin beta-2A chain	protein	307	48% helix, 15% strand	Q13885

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 16 copies · chains A, B, D, E, G, H, Q, Z, a, b, d, e, g, h, q, z
AF3 · Aluminum fluoride · ligand · 16 copies · chains A, B, D, E, G, H, Q, Z, a, b, d, e, g, h, q, z
MG · Magnesium ion · metal · 16 copies · chains A, B, D, E, G, H, Q, Z, a, b, d, e, g, h, q, 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	589	0.85	0.90	74	empty
2	557	0.85	0.90	66	empty
3	837	0.84	0.86	71	empty
4	803	0.84	0.87	73	empty
5	654	0.84	0.88	71	empty

Interfaces

67 interfaces between chains.

a–g · 4064 Å² buried · 68 hydrogen bonds · protein-protein
A–G · 4062 Å² buried · 73 hydrogen bonds · protein-protein
E–H · 3930 Å² buried · 65 hydrogen bonds · protein-protein
e–h · 3911 Å² buried · 64 hydrogen bonds · protein-protein
b–e · 3852 Å² buried · 59 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7NVN · Human TRiC complex in closed state with nanobody and tubulin bound · 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 P17987
Every structure of UniProt P78371
Every structure of UniProt P50991
Every structure of UniProt P48643
Every structure of UniProt P49368
Every structure of UniProt Q99832
Every structure of UniProt P50990
Every structure of UniProt P40227
Every structure of UniProt Q13885
Elsewhere: RCSB PDB 7NVN · PDBe 7NVN · UniProt P17987 · UniProt P78371 · UniProt P50991 · UniProt P48643 · UniProt P49368 · UniProt Q99832 · UniProt P50990 · UniProt P40227 · UniProt Q13885

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