Research workbench

Human tric complex in open state with nanobody bound

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

PDB: 7NVO
Type: protein
Length: 4,480 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-complex protein 1 subunit epsilon; T-complex protein 1 subunit eta; T-complex protein 1…
UniProt: P48643, Q99832, P50990, P40227, P49368, P17987, P50991, P78371
Ligands: ADP, AF3, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 9 distinct chains · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, e	T-complex protein 1 subunit epsilon	protein	249	53% helix, 8% strand	P48643
H, h	T-complex protein 1 subunit eta	protein	252	52% helix, 10% strand	Q99832
Q, q	T-complex protein 1 subunit theta	protein	352	54% helix, 8% strand	P50990
Z, z	T-complex protein 1 subunit zeta	protein	323	53% helix, 5% strand	P40227
G, g	T-complex protein 1 subunit gamma	protein	249	49% helix, 12% strand	P49368
A, a	T-complex protein 1 subunit alpha	protein	249	53% helix, 8% strand	P17987
D, d	T-complex protein 1 subunit delta	protein	247	49% helix, 9% strand	P50991
B, b	T-complex protein 1 subunit beta	protein	282	55% helix, 8% strand	P78371
N, n	Nanobody	protein	37	0% helix, 35% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 16 copies · chains E, H, Q, Z, G, A, D, B, e, h, q, z, g, a, d, b
AF3 · Aluminum fluoride · ligand · 12 copies · chains H, Q, Z, G, A, B, h, q, z, g, a, b
MG · Magnesium ion · metal · 16 copies · chains E, H, Q, Z, G, A, D, B, e, h, q, z, g, a, d, b

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	764	0.82	0.85	77	ADP, MG, AF3
2	744	0.82	0.85	77	ADP, MG, AF3
3	325	0.82	0.92	56	ADP, MG, AF3
4	316	0.82	0.92	53	ADP, MG, AF3
5	856	0.80	0.82	70	empty

Interfaces

36 interfaces between chains.

z–g · 1469 Å² buried · 15 hydrogen bonds · protein-protein
Z–G · 1459 Å² buried · 15 hydrogen bonds · protein-protein
H–Q · 1174 Å² buried · 19 hydrogen bonds · protein-protein
h–q · 1163 Å² buried · 18 hydrogen bonds · protein-protein
E–d · 1042 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7NVO · Human TRiC complex in open state with nanobody bound · the same entry in another collection · chain n against n, 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 P48643
Every structure of UniProt Q99832
Every structure of UniProt P50990
Every structure of UniProt P40227
Every structure of UniProt P49368
Every structure of UniProt P17987
Every structure of UniProt P50991
Every structure of UniProt P78371
Elsewhere: RCSB PDB 7NVO · PDBe 7NVO · UniProt P48643 · UniProt Q99832 · UniProt P50990 · UniProt P40227 · UniProt P49368 · UniProt P17987 · UniProt P50991 · UniProt P78371

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