SMTL ID : 8pc0.1

Sub-tomogram average of the open conformation of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x ASO- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-1,5-anhydro-D-glucitol

ASO-GAL-SIA.1: 18 residues within 4Å: Chain A: A.181, N.182, P.197, S.198, P.199, N.200, A.201, G.456, S.457, F.458, P.469, Y.470 Chain B: N.634, D.635, P.870, S.871, G.872, S.874 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.182, B:S.871, B:N.634, A:P.197, A:N.200, A:N.200, A:S.457, A:Y.470 Hydrophobic interactions: A:F.458

1 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: T.832, R.835, D.837, W.839, G.840, K.841 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.832, A:D.837, A:D.837, A:G.840, H2O.2

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: T.38, P.46, I.47, T.48, D.49, S.50, K.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.49, A:S.50, A:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sprankel, L. et al., Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium. Plos Pathog. (2023)

Release Date

2023-11-01

Peptides

Mgp-operon protein 3: A
Adhesin P1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Mgp-operon protein 3

Adhesin P1

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