MolNFT v1 · #163312 · protein

Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules

6RZA · Cytoplasmic dynein 1 heavy chain 1,DYNEIN heavy chain 7…: “Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 18 pockets (best…

PDB: 6RZA
Type: protein
Length: 1,867 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytoplasmic dynein 1 heavy chain 1,DYNEIN heavy chain 7, AXONEMAL,CYTOPLASMIC dynein 1…
UniProt: Q9JHU4, Q8WXX0, Q2XVP4, P02554
Ligands: GTP, GDP, TA1, MG
Pockets: 18 · best druggability 0.80

Structure

electron microscopy · 3 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Cytoplasmic dynein 1 heavy chain 1,DYNEIN heavy chain 7, AXONEMAL,CYTOPLASMIC dynein 1 heavy chain 1	protein	163	67% helix, 4% strand	Q9JHU4, Q8WXX0
A, C	Tubulin alpha-1B chain	protein	426	43% helix, 16% strand	Q2XVP4
B, D	Tubulin beta chain	protein	426	46% helix, 18% strand	P02554

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
TA1 · Taxol · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.80	0.95	39	GTP, MG
2	330	0.78	0.89	51	GTP, MG
3	753	0.70	0.77	67	empty
4	460	0.65	0.78	44	empty
5	50	0.65	0.96	21	empty

Interfaces

8 interfaces between chains.

C–D · 1980 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1972 Å² buried · 24 hydrogen bonds · protein-protein
X–B · 598 Å² buried · 3 hydrogen bonds · protein-protein
X–A · 492 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 471 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6RZA · Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to… · the same entry in another collection · chain X against X, 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 Q9JHU4
Every structure of UniProt Q8WXX0
Every structure of UniProt Q2XVP4
Every structure of UniProt P02554
Elsewhere: RCSB PDB 6RZA · PDBe 6RZA · UniProt Q9JHU4 · UniProt Q8WXX0 · UniProt Q2XVP4 · UniProt P02554

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