Research workbench

Human tric complex in closed state with nanobody bound (consensus MAP)

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

PDB: 7NVL
Type: protein
Length: 8,626 residues
Chains: 18
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
Ligands: ADP, AF3, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	T-complex protein 1 subunit alpha	protein	534	52% helix, 19% strand	P17987
B, b	T-complex protein 1 subunit beta	protein	526	51% helix, 18% strand	P78371
D, d	T-complex protein 1 subunit delta	protein	518	50% helix, 18% strand	P50991
E, e	T-complex protein 1 subunit epsilon	protein	534	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	520	49% helix, 19% strand	Q99832
N, n	Nanobody NB18	protein	104	6% helix, 55% strand	—
Q, q	T-complex protein 1 subunit theta	protein	529	50% helix, 18% strand	P50990
Z, z	T-complex protein 1 subunit zeta	protein	525	53% helix, 18% strand	P40227

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	1020	0.86	0.87	103	empty
2	754	0.85	0.88	73	empty
3	810	0.84	0.86	107	empty
4	1060	0.83	0.84	92	empty
5	1009	0.83	0.84	94	empty

Interfaces

62 interfaces between chains.

a–g · 4122 Å² buried · 73 hydrogen bonds · protein-protein
A–G · 4117 Å² buried · 72 hydrogen bonds · protein-protein
E–H · 3932 Å² buried · 71 hydrogen bonds · protein-protein
e–h · 3931 Å² buried · 67 hydrogen bonds · protein-protein
b–e · 3740 Å² buried · 58 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7NVL · Human TRiC complex in closed state with nanobody bound (Consensus Map) · 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
Elsewhere: RCSB PDB 7NVL · PDBe 7NVL · UniProt P17987 · UniProt P78371 · UniProt P50991 · UniProt P48643 · UniProt P49368 · UniProt Q99832 · UniProt P50990 · UniProt P40227

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