SMTL ID : 9c2k.2 (1 other biounit)

The crystal structure of HIV-1 Rev Response Element Stem-Loop II in complex with a Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.2: 12 residues within 4Å: Chain A: L.153, F.178, P.179, A.180, V.181, S.189, L.190, S.191 Chain B: Q.161, S.163, S.177, T.179 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.179, A:V.181, A:S.189, A:S.191, B:S.163, B:S.177, B:T.179 Water bridges: A:S.189 GOL.5: 3 residues within 4Å: Chain B: Q.38, P.60, F.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.38, B:Q.38 Water bridges: B:R.62 GOL.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.7: 3 residues within 4Å: Chain B: R.109, K.170, D.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.109, B:R.109, B:K.170 GOL.8: 4 residues within 4Å: Chain A: P.179 Chain B: E.162, S.163, V.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.163, B:V.164, B:V.164 GOL.9: 6 residues within 4Å: Chain A: P.135, A.137, K.226 Chain B: S.122, D.123, E.124 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.123, B:E.124, A:K.226

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

PO4.3: 3 residues within 4Å: Chain B: S.29, S.31, R.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.29, B:S.31 Water bridges: B:V.30 Salt bridges: B:R.67 PO4.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.10: 1 residues within 4Å: Chain C: G.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ojha, M. et al., Crystal structure of HIV-1 RRE SL2 in complex with Fab BL3-6. To Be Published

Release Date

2025-05-28

Peptides

BL3-6 Fab heavy chain: A
BL3-6 Fab light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BL3-6 Fab heavy chain

BL3-6 Fab light chain

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