Research workbench

P43 crystal of dctbp

Analyse P43 crystal of dctbp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZBB
Type: protein
Length: 1,020 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C4-dicarboxylate transport sensor protein dctb
EC: 2.7.13.3
UniProt: P13633
Pockets: 17 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	C4-dicarboxylate transport sensor protein dctb (EC 2.7.13.3)	protein	255	35% helix, 31% strand	P13633

Ligands and binding sites

MLA · Malonic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

17 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	949	0.72	0.76	86	empty
2	432	0.64	0.77	50	empty
3	199	0.54	0.79	30	empty
4	92	0.52	0.84	16	empty
5	107	0.48	0.80	17	empty

Interfaces

5 interfaces between chains.

C–D · 1194 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1139 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 516 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 227 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 70 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2ZBB · P43 crystal of DctBp · the same entry in another collection · chain D against D, TM-score 1.00
P13633 · AlphaFold monomer V2.0 prediction for C4-dicarboxylate transport sensor protein dctb… · a predicted model of the same protein · chain C 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 P13633
Elsewhere: RCSB PDB 2ZBB · PDBe 2ZBB · UniProt P13633

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