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Crystal structure of a neisseria meningitidis serogroup a capsular oligosaccharide bound to a functional Fab

Analyse Crystal structure of a neisseria meningitidis serogroup a capsular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y54
Type: protein
Length: 1,066 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab A1.1 H chain; Fab A1.1 L chain
Ligands: OOW, OA8, OAB, IOD
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab A1.1 H chain	protein	211	7% helix, 50% strand	—
L	Fab A1.1 L chain	protein	217	4% helix, 53% strand	—
M	Fab A1.1 H chain	protein	212	10% helix, 49% strand	—
N	Fab A1.1 L chain	protein	218	4% helix, 51% strand	—
O	Fab A1.1 H chain	protein	106	6% helix, 46% strand	—
P	Fab A1.1 L chain	protein	102	3% helix, 43% strand	—

Ligands and binding sites

OOW · {[(2R,3S,4R,5S,6R)-5-acetamido-3-hydroxy-4-(2-oxopropyl)-6-(phosphonooxy)oxan-2-yl]methoxy}phosphonic acid · ligand · 3 copies · chains H, L, M, N, O, P
OA8 · {[(2R,3S,4R,5S,6S)-3-(acetyloxy)-5-acetamido-4,6-dihydroxyoxan-2-yl]methoxy}phosphonic acid · ligand · 3 copies · chains H, L, M, N, O, P
OAB · {[(2R,3S,4R,5S,6S)-5-acetamido-3,6-dihydroxy-4-(2-oxopropyl)oxan-2-yl]methoxy}phosphonic acid · ligand · 3 copies · chains H, L, M, N, O, P
IOD · Iodide ion · ion · 9 copies · chains H, M, L, N
EDO · 1,2-ethanediol · additive · 3 copies · chains H, M

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.72	0.82	59	IOD, OOW, OA8
2	455	0.69	0.80	53	IOD
3	665	0.68	0.76	85	IOD
4	637	0.65	0.75	88	EDO, IOD
5	173	0.51	0.77	22	OOW, OA8

Interfaces

7 interfaces between chains.

M–N · 1786 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 1723 Å² buried · 13 hydrogen bonds · protein-protein
H–M · 909 Å² buried · 9 hydrogen bonds · protein-protein
O–P · 655 Å² buried · 3 hydrogen bonds · protein-protein
L–P · 549 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6Y54 · Crystal structure of a Neisseria meningitidis serogroup A capsular oligosaccharide bound… · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 6Y54 · PDBe 6Y54

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