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Crystal structure of np exonuclease C409A-pcmb complex

Analyse Crystal structure of np exonuclease C409A-pcmb complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V3C
Type: protein
Length: 402 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
EC: 3.1.13.-
UniProt: P13699
Ligands: HGB, ZN, MG
Pockets: 6 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoprotein (EC 3.1.13.-)	protein	201	38% helix, 20% strand	P13699

Ligands and binding sites

HGB · 4-(hydroxymercury)benzoic acid · ligand · chains B
ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.49	0.82	17	empty
2	207	0.49	0.75	21	empty
3	148	0.48	0.78	20	MG
4	155	0.42	0.74	20	MG
5	133	0.41	0.75	26	empty

Interfaces

1 interface between chains.

A–B · 439 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7V3C · Crystal structure of NP exonuclease C409A-PCMB complex · the same entry in another collection · chain B against B, 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 P13699
Elsewhere: RCSB PDB 7V3C · PDBe 7V3C · UniProt P13699

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