MolNFT v1 · #140035 · protein

GDP-microtubule complexed with nucleotide-free KIF5C

5XXT · Tubulin alpha-1A chain: “GDP-microtubule complexed with nucleotide-free KIF5C”. Electron microscopy, 3 ligands (GTP, GDP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #140035 on GenesisL1: 3D structure, binding sites and…

PDB: 5XXT
Type: protein
Length: 7,686 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1A chain; Tubulin beta chain
UniProt: P02550, P02554
Ligands: GTP, GDP, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O, Q	Tubulin alpha-1A chain	protein	428	44% helix, 19% strand	P02550
B, D, F, H, J, L, N, P, R	Tubulin beta chain	protein	426	49% helix, 19% strand	P02554

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
GDP · Guanosine-5'-diphosphate · ligand · 9 copies · chains B, I, D, G, F, K, H, J, L, C, N, A, P, E, R
MG · Magnesium ion · metal · 9 copies · chains A, C, E, G, I, K, M, O, Q

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	309	0.85	0.95	46	GDP
2	328	0.85	0.95	52	GTP, MG
3	341	0.84	0.94	49	GTP, MG
4	336	0.84	0.94	50	GTP, MG
5	339	0.84	0.94	50	GTP, MG

Interfaces

27 interfaces between chains.

M–N · 2081 Å² buried · 49 hydrogen bonds · protein-protein
O–P · 2080 Å² buried · 49 hydrogen bonds · protein-protein
Q–R · 2080 Å² buried · 48 hydrogen bonds · protein-protein
K–L · 2080 Å² buried · 46 hydrogen bonds · protein-protein
G–H · 2076 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

5XXT · GDP-microtubule complexed with nucleotide-free KIF5C · the same entry in another collection · chain R against R, 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 P02550
Every structure of UniProt P02554
Elsewhere: RCSB PDB 5XXT · PDBe 5XXT · UniProt P02550 · UniProt P02554

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