MolNFT v1 · #145722 · protein

Crystal structure of spaa-slh in complex with 4,6-pyr-beta-D-mannacome (P1)

6CWH · Surface (S-) layer glycoprotein: “Crystal structure of spaa-slh in complex with 4,6-pyr-beta-D-mannacome (P1)”. X-ray diffraction, 1 ligand (6LA), 8 pockets (best druggability 0.74). MolNFT v1 #145722 on GenesisL1: 3D structure…

PDB: 6CWH
Type: protein
Length: 659 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Surface (S-) layer glycoprotein
UniProt: C1JZ07
Ligands: 6LA
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Surface (S-) layer glycoprotein	protein	165	42% helix, 5% strand	C1JZ07
C	Surface (S-) layer glycoprotein	protein	164	42% helix, 5% strand	C1JZ07

Ligands and binding sites

6LA · methyl 2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.74	0.77	101	empty
2	254	0.62	0.81	40	empty
3	309	0.62	0.79	45	empty
4	54	0.41	0.82	14	6LA
5	71	0.32	0.75	16	empty

Interfaces

5 interfaces between chains.

B–C · 559 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 548 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 418 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 416 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 58 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6CWH · Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAcOMe (P1) · 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 C1JZ07
Elsewhere: RCSB PDB 6CWH · PDBe 6CWH · UniProt C1JZ07

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