MolNFT v1 · #115953 · protein

Structure of the C-terminal domains of dipz from mycobacterium tuberculosis

5CYY · Protein dipz: “Structure of the C-terminal domains of dipz from mycobacterium tuberculosis”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #115953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CYY
Type: protein
Length: 1,325 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein dipz
UniProt: P9WG63
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein dipz	protein	333	20% helix, 35% strand	P9WG63
B	Protein dipz	protein	328	20% helix, 35% strand	P9WG63
D	Protein dipz	protein	331	20% helix, 35% strand	P9WG63

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	483	0.77	0.85	70	empty
2	461	0.75	0.84	56	empty
3	161	0.61	0.84	21	empty
4	166	0.60	0.84	30	empty
5	202	0.48	0.75	32	empty

Interfaces

4 interfaces between chains.

C–D · 2227 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2127 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 203 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 135 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5CYY · Structure of the C-terminal domains of DipZ from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
P9WG63 · AlphaFold monomer V2.0 prediction for protein dipz (P9WG63) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P9WG63
Elsewhere: RCSB PDB 5CYY · PDBe 5CYY · UniProt P9WG63

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