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Crystal structure of a putative uncharacterized protein from mycobacterium marinum

Analyse Crystal structure of a putative uncharacterized protein from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S5N
Type: protein
Length: 750 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MYMAA.17060.A
UniProt: B2HFJ9
Ligands: SO4
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 29% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MYMAA.17060.A	protein	120	28% helix, 46% strand	B2HFJ9
B, E	MYMAA.17060.A	protein	128	30% helix, 43% strand	B2HFJ9
C	MYMAA.17060.A	protein	126	31% helix, 44% strand	B2HFJ9
D	MYMAA.17060.A	protein	123	30% helix, 45% strand	B2HFJ9
F	MYMAA.17060.A	protein	125	27% helix, 44% strand	B2HFJ9

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains B, C, E

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.85	0.98	27	SO4, MPD
2	167	0.84	0.98	26	SO4, MPD
3	161	0.84	0.98	27	SO4, MPD
4	250	0.79	0.91	32	SO4
5	328	0.78	0.88	41	SO4

Interfaces

8 interfaces between chains.

A–E · 1028 Å² buried · 10 hydrogen bonds · protein-protein
C–F · 1016 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 1011 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 430 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 329 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7S5N · Crystal Structure of a Putative uncharacterized protein from Mycobacterium marinum · the same entry in another collection · chain A against A, 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 B2HFJ9
Elsewhere: RCSB PDB 7S5N · PDBe 7S5N · UniProt B2HFJ9

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