SMTL ID : 3q1s.1

HIV-1 neutralizing antibody Z13e1 in complex with epitope display protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.1: 1 residues within 4Å: Chain A: N.208 No protein-ligand interaction detected (PLIP) IPA.2: 5 residues within 4Å: Chain A: E.1, L.91, L.92, P.93, Q.94 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.91 Hydrogen bonds: A:Q.94, A:Q.94 Water bridges: A:L.2

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.194, T.195, H.196, L.199, S.201, P.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.194, A:H.196, A:L.199 GOL.4: 6 residues within 4Å: Chain A: S.61, G.62, S.63, T.70, L.71, T.72 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.61, A:S.63, A:T.70, A:T.72, A:T.72 Water bridges: A:S.63 GOL.5: 6 residues within 4Å: Chain A: Q.35, Q.36, K.37, Q.40, A.41, R.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.35, A:K.37, A:K.37, A:Q.40 GOL.6: 3 residues within 4Å: Chain A: P.57, A.58, R.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.58, A:R.59, A:R.59 GOL.7: 4 residues within 4Å: Chain B: I.73, S.74, K.75, N.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.75 GOL.8: 6 residues within 4Å: Chain B: R.38, Q.46, L.48, N.60, S.62, L.63 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:S.62 Water bridges: B:Q.46, B:Q.46, B:N.60 GOL.9: 5 residues within 4Å: Chain B: I.52, G.54, G.55, T.56 Chain C: W.38 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.37, B:T.56, B:T.56 GOL.10: 4 residues within 4Å: Chain A: Q.94 Chain B: E.43, R.44, Q.46 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.44, B:R.44, B:Q.46, B:Q.46, A:Q.94 GOL.11: 7 residues within 4Å: Chain B: L.106, N.107, Y.108 Chain C: I.41, T.42, D.43, R.45 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:L.106, C:D.43, C:R.45 GOL.12: 7 residues within 4Å: Chain B: N.31, I.100 Chain C: K.33, E.34, A.35, W.36, N.37 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.33, C:W.36, C:N.37, C:N.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanfield, R.L. et al., Structure-Based Design of a Protein Immunogen that Displays an HIV-1 gp41 Neutralizing Epitope. J.Mol.Biol. (2011)

Release Date

2011-11-02

Peptides

Z13e1 Fab light chain: A
Z13e1 Fab heavy chain: B
Interleukin-22: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Z13e1 Fab light chain

Z13e1 Fab heavy chain

Interleukin-22

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