MolNFT v1 · #27229 · protein

Crystal structure of lpda (RV3303C) from mycobacterium tuberculosis

1XDI · RV3303C-lpda: “Crystal structure of lpda (RV3303C) from mycobacterium tuberculosis”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.83). MolNFT v1 #27229 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1XDI
Type: protein
Length: 918 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RV3303C-lpda
UniProt: O53355
Ligands: FAD
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RV3303C-lpda	protein	459	34% helix, 26% strand	O53355

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1081	0.83	0.84	78	empty
2	182	0.80	0.95	33	empty
3	210	0.78	0.92	31	empty
4	761	0.78	0.82	88	FAD
5	777	0.77	0.81	86	FAD

Interfaces

1 interface between chains.

A–B · 3632 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

1XDI · Crystal structure of LpdA (Rv3303c) from Mycobacterium tuberculosis · 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 O53355
Elsewhere: RCSB PDB 1XDI · PDBe 1XDI · UniProt O53355

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