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Synthetic haliangium ochraceum bmc shell

Analyse Synthetic haliangium ochraceum bmc shell in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NER
Type: protein
Length: 5,521 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bmc-H tandem fusion protein
UniProt: D0LID5
Ligands: SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 38% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H, V, Y	Bmc-H tandem fusion protein	protein	185	38% helix, 35% strand	D0LID5
B, C, K, Z, c, d	Bmc-H tandem fusion protein	protein	185	38% helix, 36% strand	D0LID5
D, S	Bmc-H tandem fusion protein	protein	182	38% helix, 35% strand	D0LID5
E	Bmc-H tandem fusion protein	protein	186	38% helix, 34% strand	D0LID5
F, I, J, O, Q, R, T, U, W, a	Bmc-H tandem fusion protein	protein	184	38% helix, 34% strand	D0LID5
G, P	Bmc-H tandem fusion protein	protein	183	38% helix, 36% strand	D0LID5
L, M, N	Bmc-H tandem fusion protein	protein	183	38% helix, 36% strand	D0LID5
X	Bmc-H tandem fusion protein	protein	184	38% helix, 35% strand	D0LID5
b	Bmc-H tandem fusion protein	protein	182	38% helix, 36% strand	D0LID5

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1132	0.83	0.84	99	empty
2	591	0.79	0.85	51	empty
3	520	0.78	0.85	45	empty
4	496	0.78	0.86	45	empty
5	493	0.78	0.85	42	empty

Interfaces

63 interfaces between chains.

S–U · 992 Å² buried · 14 hydrogen bonds · protein-protein
V–X · 990 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 987 Å² buried · 14 hydrogen bonds · protein-protein
P–R · 987 Å² buried · 13 hydrogen bonds · protein-protein
G–I · 984 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6NER · Synthetic Haliangium ochraceum BMC shell · the same entry in another collection · chain I against I, 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 D0LID5
Elsewhere: RCSB PDB 6NER · PDBe 6NER · UniProt D0LID5

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