SMTL ID : 7n05.1

Crystal structure of the F240 antibody fragment bound to the HIV-1 gp41 immunodominant region

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 15 residues within 4Å: Chain A: L.153, F.178, P.179, A.180, V.181, S.189, L.190, S.191 Chain B: V.139, Q.166, E.167, S.168, S.182, S.183, T.184 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:P.179, A:S.191, B:Q.166, B:S.168, B:S.182, B:T.184 GOL.3: 11 residues within 4Å: Chain B: Q.43, R.45, K.51, L.53, G.63, V.64, A.65, R.67, F.68, E.87, D.88 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.43, B:R.45, B:K.51, B:A.65, B:R.67, B:E.87, B:D.88 Water bridges: B:G.63

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: V.175, H.176, T.177 Chain B: T.170, E.171, D.173 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:V.175, A:T.177, A:T.177, B:T.170, B:S.174 Salt bridges: A:H.176 Hydrogen bonds: B:D.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, J.D. et al., Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies. Commun Biol (2022)

Release Date

2022-03-30

Peptides

Fab F240 heavy chain: A
Fab F240 light chain: B
HIV-1 gp41 immunodominant region: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

Fab F240 heavy chain

Fab F240 light chain

HIV-1 gp41 immunodominant region

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