MolNFT v1 · #88176 · protein

Crystal structure of RV3378C

4CMX: “Crystal structure of RV3378C”. X-ray diffraction, 1 ligand (BHC), 7 pockets (best druggability 0.83). MolNFT v1 #88176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CMX
Type: protein
Length: 584 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RV3378C
UniProt: O50407
Ligands: BHC
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RV3378C	protein	293	48% helix, 15% strand	O50407
B	RV3378C	protein	291	49% helix, 15% strand	O50407

Ligands and binding sites

BHC · Benzene hexacarboxylic acid · ligand · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.83	0.94	38	empty
2	113	0.79	0.98	26	empty
3	111	0.79	0.98	23	empty
4	396	0.66	0.80	50	EDO, BHC
5	294	0.66	0.82	42	BHC, PEG

Interfaces

1 interface between chains.

A–B · 3911 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

4CMX · Crystal structure of Rv3378c · 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 O50407
Elsewhere: RCSB PDB 4CMX · PDBe 4CMX · UniProt O50407

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