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Structure of B. subtilis genomic dutpase yncf in complex with du, ppi and mg in P1

Analyse Structure of B. subtilis genomic dutpase yncf in complex with du, ppi and mg in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4APZ
Type: protein
Length: 6,822 residues
Chains: 48
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf
EC: 3.6.1.23
UniProt: O31801
Ligands: DUR, POP, MG, PO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 2, 3, 4, 5, 6, 7, 8, 9, B, C, D, E, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, Z, c, d, e, f, g, h, i, k, l, m	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23)	protein	142	4% helix, 42% strand	O31801
A, F, Q, a, b, j	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase yncf (EC 3.6.1.23)	protein	143	3% helix, 42% strand	O31801

Ligands and binding sites

DUR · 2'-deoxyuridine · ligand · 48 copies · chains 1, Y, Z, 2, 3, 4, 5, 6, 7, 8, 9, a, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, b, c, d, e, f, g, h, i, j, k, l, m
POP · Pyrophosphate 2- · ligand · 48 copies · chains 1, Y, 2, 3, 4, 5, 7, 6, 8, 9, a, A, C, B, D, E, F, G, I, H, J, K, L, M, N, O, P, R, Q, S, U, T, V, W, X, Z, b, d, c, e, g, f, h, j, i, k, m, l
MG · Magnesium ion · metal · 48 copies · chains 1, Y, 2, 3, 4, 5, 7, 6, 8, 9, a, A, C, B, D, E, F, G, I, H, J, K, L, M, N, O, P, R, Q, S, U, T, V, W, X, Z, b, d, c, e, g, f, h, j, i, k, m, l
PO4 · Phosphate ion · ion · 2 copies · chains e, f, g, k, l, m

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.81	0.85	105	POP, MG, DUR
2	134	0.78	0.96	32	DUR, POP, MG
3	130	0.78	0.97	31	DUR, POP, MG
4	122	0.78	0.97	29	DUR, POP, MG
5	130	0.78	0.96	29	DUR, POP, MG

Interfaces

154 interfaces between chains.

8–a · 2329 Å² buried · 48 hydrogen bonds · protein-protein
P–Q · 2309 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 2307 Å² buried · 51 hydrogen bonds · protein-protein
i–j · 2302 Å² buried · 46 hydrogen bonds · protein-protein
b–d · 2298 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

4APZ · Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1 · the same entry in another collection · chain 7 against 7, TM-score 1.00

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Every structure of UniProt O31801
Elsewhere: RCSB PDB 4APZ · PDBe 4APZ · UniProt O31801

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