MolNFT v2 · #205753 · protein

In situ structure of the Nitrosopumilus maritimus S-layer - Six-fold symmetry (C6)

8C8O · Cell surface protein: “In situ structure of the Nitrosopumilus maritimus S-layer - Six-fold symmetry (C6)”. Electron microscopy at 3.4, 20 pockets (best druggability 0.79). MolNFT v2 #205753 on GenesisL1: 3D structure, binding sites…

PDB: 8C8O
Type: protein
Length: 6,318 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Nitrosopumilus maritimus SCM1
Molecule: Cell surface protein
UniProt: A9A4Y9
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · resolution 3.4 · 1 distinct chain · 9% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cell surface protein	protein	1053	9% helix, 37% strand	A9A4Y9

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	1152	0.79	0.81	124	empty
2	940	0.78	0.81	96	empty
3	611	0.77	0.83	73	empty
4	927	0.76	0.80	92	empty
5	901	0.76	0.80	94	empty

Interfaces

6 interfaces between chains.

A–B · 1881 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1880 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1879 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 1879 Å² buried · 23 hydrogen bonds · protein-protein
A–F · 1867 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

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 A9A4Y9
Elsewhere: RCSB PDB 8C8O · PDBe 8C8O · UniProt A9A4Y9

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