MolNFT v1 · #38920 · protein

Trypsin-modified elongation factor tu in complex with tetracycline at 2.8 ångström resolution

2HDN · Elongation factor ef-tu: “Trypsin-modified elongation factor tu in complex with tetracycline at 2.8 ångström resolution”. X-ray diffraction, 3 ligands (GDP, TAC, MG), 20 pockets (best druggability 0.74). MolNFT v1 #38920 on…

PDB: 2HDN
Type: protein
Length: 2,208 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor ef-tu
UniProt: P0A6N1
Ligands: GDP, TAC, MG
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Elongation factor ef-tu	protein	33	48% helix, 21% strand	P0A6N1
B, D, F, H, J, L	Elongation factor ef-tu	protein	335	20% helix, 40% strand	P0A6N1

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
TAC · Tetracycline · ligand · 6 copies · chains A, B, D, C, E, F, G, H, I, J, L, K
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	908	0.74	0.78	69	empty
2	1020	0.69	0.74	95	TAC
3	212	0.63	0.83	38	empty
4	517	0.59	0.74	69	TAC
5	124	0.55	0.83	28	empty

Interfaces

17 interfaces between chains.

C–D · 1933 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1929 Å² buried · 29 hydrogen bonds · protein-protein
I–J · 1925 Å² buried · 29 hydrogen bonds · protein-protein
E–F · 1917 Å² buried · 30 hydrogen bonds · protein-protein
K–L · 1917 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2HDN · Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom… · the same entry in another collection · chain A against A, 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 P0A6N1
Elsewhere: RCSB PDB 2HDN · PDBe 2HDN · UniProt P0A6N1

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