MolNFT v1 · #25359 · protein

Crystal structure of exodeoxyribonuclease VII small subunit (NP_881400.1) from bordetella pertussis at 2.40 a resolution

1VP7: “Crystal structure of exodeoxyribonuclease VII small subunit (NP_881400.1) from bordetella pertussis at 2.40 a…”. X-ray diffraction, 5 pockets (best druggability 0.40). MolNFT v1 #25359 on GenesisL1: 3D structure, binding sites and…

PDB: 1VP7
Type: protein
Length: 417 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exodeoxyribonuclease VII small subunit
EC: 3.1.11.6
UniProt: Q7W7Q2
Pockets: 5 · best druggability 0.40

Structure

x-ray diffraction · 6 distinct chains · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	68	78% helix, 1% strand	Q7W7Q2
B	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	77	71% helix, 1% strand	Q7W7Q2
C	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	71	73% helix, 1% strand	Q7W7Q2
D	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	69	77% helix, 0% strand	Q7W7Q2
E	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	67	79% helix, 1% strand	Q7W7Q2
F	Exodeoxyribonuclease VII small subunit (EC 3.1.11.6)	protein	65	82% helix, 0% strand	Q7W7Q2

Pockets

5 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	110	0.40	0.75	16	empty
2	105	0.37	0.74	18	empty
3	93	0.33	0.73	15	empty
4	74	0.31	0.74	19	empty
5	67	0.31	0.75	12	empty

Interfaces

5 interfaces between chains.

A–B · 1301 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 1188 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1069 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 521 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 497 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

1VP7 · Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella… · the same entry in another collection · chain F against F, TM-score 1.00
Q7W7Q2 · AlphaFold monomer V2.0 prediction for exodeoxyribonuclease 7 small subunit (Q7W7Q2) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 Q7W7Q2
Elsewhere: RCSB PDB 1VP7 · PDBe 1VP7 · UniProt Q7W7Q2

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