MolNFT v1 · #10710 · protein

Crystal structure of actin filament capping protein capz

1IZN · Capz alpha-1 subunit: “Crystal structure of actin filament capping protein capz”. X-ray diffraction, 1 ligand (NO3), 12 pockets (best druggability 0.74). MolNFT v1 #10710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IZN
Type: protein
Length: 1,088 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capz alpha-1 subunit; Capz beta-1 subunit
UniProt: P13127, P14315
Ligands: NO3
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capz alpha-1 subunit	protein	275	38% helix, 30% strand	P13127
B, D	Capz beta-1 subunit	protein	270	42% helix, 32% strand	P14315
C	Capz alpha-1 subunit	protein	273	40% helix, 32% strand	P13127

Ligands and binding sites

NO3 · Nitrate ion · ion · 4 copies · chains A, B, D, C

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

Pockets

12 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	884	0.74	0.78	108	NO3
2	304	0.66	0.81	45	NO3
3	291	0.65	0.81	40	NO3
4	201	0.55	0.79	23	empty
5	235	0.54	0.77	29	empty

Interfaces

6 interfaces between chains.

C–D · 4017 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 3924 Å² buried · 60 hydrogen bonds · protein-protein
B–D · 839 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 171 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 63 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1IZN · Crystal Structure of Actin Filament Capping Protein CapZ · the same entry in another collection · chain D against D, TM-score 1.00
P13127 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit alpha-1 (P13127) · a predicted model of the same protein · chain C against A, TM-score 0.92
P14315 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit beta isoforms 1 and… · a predicted model of the same protein · chain D against A, TM-score 0.91

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 P13127
Every structure of UniProt P14315
Elsewhere: RCSB PDB 1IZN · PDBe 1IZN · UniProt P13127 · UniProt P14315

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