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Cryoem structure of a respiratory membrane-bound hydrogenase

Analyse Cryoem structure of a respiratory membrane-bound hydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CFW
Type: protein
Length: 2,530 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monovalent CATION/H+ antiporter subunit D; Monovalent CATION/H+ antiporter subunit C; Mbh…
EC: 1.12.7.2
UniProt: I6UQL5, I6UZU1, Q8U104, I6U847, I6UQM0, I6TXN5, I6TXN1, I6V287, I6UQL1, I6UZT7, Q8U0Z8, Q8U0Z7, Q8U0Z6, I6U851
Ligands: SF4, NFU
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 14 distinct chains · 52% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Monovalent CATION/H+ antiporter subunit D	protein	505	61% helix, 2% strand	I6UQL5
G	Monovalent CATION/H+ antiporter subunit C	protein	113	55% helix, 6% strand	I6UZU1
D	Mbh subunit	protein	78	82% helix, 0% strand	Q8U104
I	Mbh subunit	protein	114	51% helix, 3% strand	I6U847
M	MBH13 NADH dehydrogenase subunit	protein	317	61% helix, 1% strand	I6UQM0
F	Monovalent CATION/H+ antiporter subunit B	protein	145	58% helix, 0% strand	I6TXN5
A	Monovalent CATION/H+ antiporter subunit E	protein	165	46% helix, 10% strand	I6TXN1
E	Mbh subunit	protein	93	67% helix, 1% strand	I6V287
C	Monovalent CATION/H+ antiporter subunit G	protein	114	74% helix, 1% strand	I6UQL1
B	Monovalent CATION/H+ antiporter subunit F	protein	82	77% helix, 0% strand	I6UZT7
J	Probable membrane-bound hydrogenase subunit mbhj (EC 1.12.7.2)	protein	143	28% helix, 12% strand	Q8U0Z8
K	Membrane-bound hydrogenase subunit beta (EC 1.12.7.2)	protein	166	22% helix, 16% strand	Q8U0Z7
L	Membrane-bound hydrogenase subunit alpha (EC 1.12.7.2)	protein	374	44% helix, 10% strand	Q8U0Z6
N	NADH-plastoquinone oxidoreductase subunit	protein	121	21% helix, 13% strand	I6U851

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 3 copies · chains J, L, N
NFU · formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) · ligand · chains L

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	1133	0.85	0.86	88	empty
2	124	0.78	0.96	27	empty
3	1173	0.78	0.79	79	empty
4	1054	0.77	0.79	65	empty
5	87	0.77	0.98	22	SF4

Interfaces

34 interfaces between chains.

G–E · 2022 Å² buried · 6 hydrogen bonds · protein-protein
H–E · 2017 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 1906 Å² buried · 3 hydrogen bonds · protein-protein
K–L · 1893 Å² buried · 7 hydrogen bonds · protein-protein
C–B · 1858 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6CFW · cryoEM structure of a respiratory membrane-bound hydrogenase · the same entry in another collection · chain N against N, 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 I6UQL5
Every structure of UniProt I6UZU1
Every structure of UniProt Q8U104
Every structure of UniProt I6U847
Every structure of UniProt I6UQM0
Every structure of UniProt I6TXN5
Every structure of UniProt I6TXN1
Every structure of UniProt I6V287
Every structure of UniProt I6UQL1
Every structure of UniProt I6UZT7
Every structure of UniProt Q8U0Z8
Every structure of UniProt Q8U0Z7
Every structure of UniProt Q8U0Z6
Every structure of UniProt I6U851
Elsewhere: RCSB PDB 6CFW · PDBe 6CFW · UniProt I6UQL5 · UniProt I6UZU1 · UniProt Q8U104 · UniProt I6U847 · UniProt I6UQM0 · UniProt I6TXN5 · UniProt I6TXN1 · UniProt I6V287 · UniProt I6UQL1 · UniProt I6UZT7 · UniProt Q8U0Z8 · UniProt Q8U0Z7 · UniProt Q8U0Z6 · UniProt I6U851

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