MolNFT v1 · #116750 · protein

ATP synthase from paracoccus denitrificans

5DN6 · Chain a: “ATP synthase from paracoccus denitrificans”. X-ray diffraction, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #116750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DN6
Type: protein
Length: 4,682 residues
Chains: 29
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chain a; Chain B; Chain C; ATP synthase subunit alpha; ATP synthase subunit beta; ATP…
EC: 7.1.2.2
UniProt: A1B8N8, A1B8P0, A1B8N9, A1B8N7, A1B8P1, A1B618, A1B619, A1B602
Ligands: ATP, ADP, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 18 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Chain a	protein	20	45% helix, 0% strand	—
2	Chain B	protein	15	80% helix, 0% strand	—
3	Chain C	protein	19	89% helix, 0% strand	—
A	ATP synthase subunit alpha (EC 7.1.2.2)	protein	505	42% helix, 20% strand	A1B8N8
B	ATP synthase subunit alpha (EC 7.1.2.2)	protein	496	43% helix, 19% strand	A1B8N8
C	ATP synthase subunit alpha (EC 7.1.2.2)	protein	484	42% helix, 20% strand	A1B8N8
D	ATP synthase subunit beta (EC 7.1.2.2)	protein	470	38% helix, 21% strand	A1B8P0
E	ATP synthase subunit beta (EC 7.1.2.2)	protein	466	37% helix, 21% strand	A1B8P0
F	ATP synthase subunit beta (EC 7.1.2.2)	protein	466	39% helix, 22% strand	A1B8P0
G	ATP synthase gamma chain	protein	260	67% helix, 12% strand	A1B8N9
H	ATP synthase subunit delta	protein	110	75% helix, 0% strand	A1B8N7
I	ATP synthase epsilon chain	protein	75	0% helix, 53% strand	A1B8P1
J, K, L, M, N, O, P, Q, R, S, T, U	ATP synthase F0 subcomplex C subunit	protein	74	95% helix, 0% strand	A1B618
V	Chain V	protein	78	97% helix, 0% strand	—
W	Chain W	protein	124	94% helix, 0% strand	—
X	ATP synthase subunit A,ATP synthase subunit A,ATP synthase subunit A,ATP synthase subunit a	protein	98	86% helix, 0% strand	A1B619
Y	Chain Y	protein	54	87% helix, 0% strand	—
Z	Zeta inhibitor protein	protein	54	80% helix, 0% strand	A1B602

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, C, F, B
ADP · Adenosine-5'-diphosphate · ligand · chains B, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F

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	1109	0.87	0.88	116	ADP, MG
2	720	0.85	0.88	58	ATP, MG
3	1074	0.84	0.85	125	ATP, MG
4	800	0.84	0.87	82	ATP, MG
5	654	0.83	0.87	69	empty

Interfaces

54 interfaces between chains.

A–D · 2634 Å² buried · 32 hydrogen bonds · protein-protein
C–F · 2404 Å² buried · 23 hydrogen bonds · protein-protein
B–F · 2258 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2189 Å² buried · 32 hydrogen bonds · protein-protein
A–E · 1983 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

5DN6 · ATP synthase from Paracoccus denitrificans · the same entry in another collection · chain G against G, 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 A1B8N8
Every structure of UniProt A1B8P0
Every structure of UniProt A1B8N9
Every structure of UniProt A1B8N7
Every structure of UniProt A1B8P1
Every structure of UniProt A1B618
Every structure of UniProt A1B619
Every structure of UniProt A1B602
Elsewhere: RCSB PDB 5DN6 · PDBe 5DN6 · UniProt A1B8N8 · UniProt A1B8P0 · UniProt A1B8N9 · UniProt A1B8N7 · UniProt A1B8P1 · UniProt A1B618 · UniProt A1B619 · UniProt A1B602

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