MolNFT v1 · #86850 · protein

Crystal structure of cpxahdc (monoclinic form 2)

4BIY · Sensor protein cpxa: “Crystal structure of cpxahdc (monoclinic form 2)”. X-ray diffraction, 2 ligands (ADP, SO4), 13 pockets (best druggability 0.83). MolNFT v1 #86850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BIY
Type: protein
Length: 893 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensor protein cpxa
EC: 2.7.13.3
UniProt: P0AE82
Ligands: ADP, SO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Sensor protein cpxa (EC 2.7.13.3)	protein	228	52% helix, 19% strand	P0AE82
B	Sensor protein cpxa (EC 2.7.13.3)	protein	221	55% helix, 20% strand	P0AE82
D	Sensor protein cpxa (EC 2.7.13.3)	protein	216	57% helix, 20% strand	P0AE82

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	662	0.83	0.88	60	SO4
2	502	0.78	0.85	59	ADP
3	312	0.77	0.88	40	empty
4	564	0.72	0.80	58	empty
5	156	0.68	0.88	24	ADP

Interfaces

6 interfaces between chains.

A–B · 2725 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2553 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1868 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 734 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 532 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4BIY · Crystal structure of CpxAHDC (monoclinic form 2) · the same entry in another collection · chain D against D, TM-score 1.00
P0AE82 · AlphaFold monomer V2.0 prediction for sensor histidine kinase cpxa (P0AE82) · a predicted model of the same protein · chain B against A, TM-score 0.76

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 P0AE82
Elsewhere: RCSB PDB 4BIY · PDBe 4BIY · UniProt P0AE82

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