Research workbench

Human tric complex in closed state with nanobody NB18, actin and PHLP2A bound

Analyse Human tric complex in closed state with nanobody NB18, actin and PHLP2A bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NVM
Type: protein
Length: 9,219 residues
Chains: 20
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, P63261, Q9H2J4
Ligands: ADP, AF3, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 18 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-complex protein 1 subunit alpha	protein	536	52% helix, 19% strand	P17987
B	T-complex protein 1 subunit beta	protein	526	50% helix, 18% strand	P78371
D, d	T-complex protein 1 subunit delta	protein	520	51% helix, 18% strand	P50991
E	T-complex protein 1 subunit epsilon	protein	535	49% helix, 17% strand	P48643
G	T-complex protein 1 subunit gamma	protein	526	49% helix, 16% strand	P49368
H	T-complex protein 1 subunit eta	protein	528	48% helix, 18% strand	Q99832
N, n	Nanobody NB18	protein	119	3% helix, 50% strand	—
Q	T-complex protein 1 subunit theta	protein	538	49% helix, 17% strand	P50990
Z	T-complex protein 1 subunit zeta	protein	525	53% helix, 18% strand	P40227
a	T-complex protein 1 subunit alpha	protein	532	51% helix, 19% strand	P17987
b	T-complex protein 1 subunit beta	protein	525	51% helix, 19% strand	P78371
e	T-complex protein 1 subunit epsilon	protein	540	49% helix, 16% strand	P48643
g	T-complex protein 1 subunit gamma	protein	538	47% helix, 17% strand	P49368
h	T-complex protein 1 subunit eta	protein	525	49% helix, 18% strand	Q99832
q	T-complex protein 1 subunit theta	protein	533	50% helix, 17% strand	P50990
z	T-complex protein 1 subunit zeta	protein	527	53% helix, 18% strand	P40227
K	Actin, cytoplasmic 2	protein	317	40% helix, 15% strand	P63261
P	Phosducin-like protein 3	protein	190	41% helix, 15% strand	Q9H2J4

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	987	0.89	0.91	143	empty
2	606	0.85	0.90	67	empty
3	871	0.85	0.87	104	empty
4	916	0.84	0.86	90	empty
5	1006	0.84	0.85	88	empty

Interfaces

80 interfaces between chains.

a–g · 4454 Å² buried · 85 hydrogen bonds · protein-protein
A–G · 4277 Å² buried · 70 hydrogen bonds · protein-protein
e–h · 3931 Å² buried · 65 hydrogen bonds · protein-protein
E–H · 3906 Å² buried · 62 hydrogen bonds · protein-protein
b–e · 3753 Å² buried · 54 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7NVM · Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound · 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 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 P63261
Every structure of UniProt Q9H2J4
Elsewhere: RCSB PDB 7NVM · PDBe 7NVM · UniProt P17987 · UniProt P78371 · UniProt P50991 · UniProt P48643 · UniProt P49368 · UniProt Q99832 · UniProt P50990 · UniProt P40227 · UniProt P63261 · UniProt Q9H2J4

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