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Crystal structure of hg-bound sufb-sufc-sufd complex from escherichia COLI

Analyse Crystal structure of hg-bound sufb-sufc-sufd complex from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AWG
Type: protein
Length: 2,415 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fes cluster assembly protein sufb; Fes cluster assembly protein sufd; Probable…
UniProt: P77522, P77689, P77499
Ligands: HG
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 8 distinct chains · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fes cluster assembly protein sufb	protein	380	23% helix, 36% strand	P77522
B	Fes cluster assembly protein sufd	protein	361	15% helix, 46% strand	P77689
C	Probable ATP-dependent transporter sufc	protein	237	36% helix, 27% strand	P77499
D	Probable ATP-dependent transporter sufc	protein	235	34% helix, 26% strand	P77499
E	Fes cluster assembly protein sufb	protein	372	23% helix, 39% strand	P77522
F	Fes cluster assembly protein sufd	protein	355	17% helix, 45% strand	P77689
G	Probable ATP-dependent transporter sufc	protein	239	35% helix, 27% strand	P77499
H	Probable ATP-dependent transporter sufc	protein	236	35% helix, 25% strand	P77499

Ligands and binding sites

HG · Mercury (II) ion · metal · 4 copies · chains A, B, E, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.74	0.99	18	empty
2	143	0.58	0.83	33	empty
3	117	0.54	0.83	21	empty
4	224	0.53	0.77	32	empty
5	166	0.49	0.77	24	empty

Interfaces

7 interfaces between chains.

E–F · 1459 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1396 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 1087 Å² buried · 6 hydrogen bonds · protein-protein
E–G · 1004 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 971 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5AWG · Crystal structure of Hg-bound SufB-SufC-SufD complex from Escherichia coli · the same entry in another collection · chain H against H, TM-score 1.00
P77689 · AlphaFold monomer V2.0 prediction for fes cluster assembly protein sufd (P77689) · a predicted model of the same protein · chain B against A, TM-score 0.98
P77499 · AlphaFold monomer V2.0 prediction for probable ATP-dependent transporter sufc (P77499) · a predicted model of the same protein · chain H against A, TM-score 0.97

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 P77522
Every structure of UniProt P77689
Every structure of UniProt P77499
Elsewhere: RCSB PDB 5AWG · PDBe 5AWG · UniProt P77522 · UniProt P77689 · UniProt P77499

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