SMTL ID : 5mza.1

The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain B: I.10, N.118, L.165, P.167, Q.168 No protein-ligand interaction detected (PLIP)

1 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.2: 6 residues within 4Å: Chain A: C.79, K.153, Y.154, Q.157, H.158, K.161 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.157 Salt bridges: A:K.153, A:H.158, A:K.161, A:K.161, A:K.161

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 6 residues within 4Å: Chain A: H.395, V.397 Chain B: P.86, E.87, E.174, N.175 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.86, B:N.175 Hydrophobic interactions: A:V.397 NAG.4: 3 residues within 4Å: Chain B: G.154, N.156, Q.181 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.154

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.5: 4 residues within 4Å: Chain B: R.125, K.128, R.149, H.152 7 PLIP interactions: 7 interactions with chain B Salt bridges: B:R.125, B:R.125, B:K.128, B:K.128, B:R.149, B:R.149, B:H.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lennartz, F. et al., Structure-Guided Identification of a Family of Dual Receptor-Binding PfEMP1 that Is Associated with Cerebral Malaria. Cell Host Microbe (2017)

Release Date

2017-03-22

Peptides

Erythrocyte membrane protein 1 (PfEMP1): A
Intercellular adhesion molecule 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Erythrocyte membrane protein 1 (PfEMP1)

Intercellular adhesion molecule 1

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