MolNFT v1 · #59875 · protein

The crystal structure of lepa

3CB4 · GTP-binding protein lepa: “The crystal structure of lepa”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #59875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3CB4
Type: protein
Length: 3,150 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP-binding protein lepa
UniProt: P60785
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, E, F	GTP-binding protein lepa	protein	525	26% helix, 38% strand	P60785

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	1124	0.75	0.78	113	empty
2	859	0.73	0.78	86	empty
3	751	0.72	0.78	70	empty
4	698	0.70	0.78	64	empty
5	627	0.70	0.78	74	empty

Interfaces

11 interfaces between chains.

C–F · 1356 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1329 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1322 Å² buried · 19 hydrogen bonds · protein-protein
B–F · 727 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 705 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3CB4 · The Crystal Structure of LepA · the same entry in another collection · chain B against B, TM-score 1.00
P60785 · AlphaFold monomer V2.0 prediction for elongation factor 4 (P60785) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P60785
Elsewhere: RCSB PDB 3CB4 · PDBe 3CB4 · UniProt P60785

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