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Structure of the membrane-bound sulfane sulfur reductase (mbs), an archaeal respiratory membrane complex

Analyse Structure of the membrane-bound sulfane sulfur reductase (mbs), an archaeal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U8Y
Type: protein
Length: 6,140 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monovalent CATION/H+ antiporter subunit E; Monovalent CATION/H+ antiporter subunit F…
EC: 1.6.99.5
UniProt: I6UQN5, I6UZW2, I6TXQ5, I6V2A4, I6U860, I6UQN0, I6UZV7, I6TXQ1, I6UZV3, I6TXP7, I6V297, I6V2A1, I6U853
Ligands: SF4
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 13 distinct chains · 51% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	Monovalent CATION/H+ antiporter subunit E	protein	161	45% helix, 6% strand	I6UQN5
B, b	Monovalent CATION/H+ antiporter subunit F	protein	79	71% helix, 0% strand	I6UZW2
C, c	Monovalent CATION/H+ antiporter subunit G	protein	112	73% helix, 0% strand	I6TXQ5
D, d	DUF4040 domain-containing protein	protein	89	57% helix, 0% strand	I6V2A4
E, e	Monovalent CATION/H+ antiporter subunit B	protein	232	57% helix, 1% strand	I6U860
G, g	Monovalent CATION/H+ antiporter subunit C	protein	110	60% helix, 2% strand	I6UQN0
H, h	NADH dehydrogenase subunit N	protein	487	60% helix, 2% strand	I6UZV7
X, x	NADH dehydrogenase subunit M	protein	603	57% helix, 1% strand	I6TXQ1
J, j	NADH dehydrogenase subunit B (EC 1.6.99.5)	protein	177	38% helix, 8% strand	I6UZV3
K, k	NADH dehydrogenase subunit C (EC 1.6.99.5)	protein	170	21% helix, 19% strand	I6TXP7
L, l	NADH dehydrogenase subunit D (EC 1.6.99.5)	protein	373	36% helix, 11% strand	I6V297
M, m	NADH dehydrogenase subunit	protein	301	71% helix, 0% strand	I6V2A1
N, n	NADH dehydrogenase subunit I (EC 1.6.99.5)	protein	176	13% helix, 15% strand	I6U853

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains J, L, N, j, l, n

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	640	0.89	0.94	84	empty
2	620	0.89	0.94	83	empty
3	1053	0.79	0.80	69	empty
4	855	0.79	0.81	70	empty
5	1085	0.78	0.79	68	empty

Interfaces

80 interfaces between chains.

X–M · 3506 Å² buried · 22 hydrogen bonds · protein-protein
x–m · 3498 Å² buried · 17 hydrogen bonds · protein-protein
h–x · 2883 Å² buried · 8 hydrogen bonds · protein-protein
H–X · 2871 Å² buried · 8 hydrogen bonds · protein-protein
E–H · 2386 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6U8Y · Structure of the membrane-bound sulfane sulfur reductase (MBS), an archaeal respiratory… · 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 I6UQN5
Every structure of UniProt I6UZW2
Every structure of UniProt I6TXQ5
Every structure of UniProt I6V2A4
Every structure of UniProt I6U860
Every structure of UniProt I6UQN0
Every structure of UniProt I6UZV7
Every structure of UniProt I6TXQ1
Every structure of UniProt I6UZV3
Every structure of UniProt I6TXP7
Every structure of UniProt I6V297
Every structure of UniProt I6V2A1
Every structure of UniProt I6U853
Elsewhere: RCSB PDB 6U8Y · PDBe 6U8Y · UniProt I6UQN5 · UniProt I6UZW2 · UniProt I6TXQ5 · UniProt I6V2A4 · UniProt I6U860 · UniProt I6UQN0 · UniProt I6UZV7 · UniProt I6TXQ1 · UniProt I6UZV3 · UniProt I6TXP7 · UniProt I6V297 · UniProt I6V2A1 · UniProt I6U853

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