SMTL ID : 1n0x.1

Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-oligomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: S.122, D.123, E.124 Chain B: P.137, K.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:E.124, A:E.124, A:E.124 GOL.4: 3 residues within 4Å: Chain B: Y.102, S.103, W.104 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.103, B:W.104 GOL.5: 4 residues within 4Å: Chain B: I.51, G.56, T.71, A.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.72 GOL.6: 3 residues within 4Å: Chain C: P.8, G.9, T.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.9, C:T.10, C:T.10 GOL.7: 1 residues within 4Å: Chain C: D.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.61 GOL.9: 7 residues within 4Å: Chain D: N.31, F.32, V.33, V.99, Y.102, N.111, Y.112 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.31, D:V.33, D:N.111, D:Y.112, D:Y.112 GOL.10: 2 residues within 4Å: Chain D: S.7, G.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.8 Water bridges: D:G.8 GOL.11: 2 residues within 4Å: Chain D: Y.54, N.55 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.55

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain B: R.87, S.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.88, B:S.88 Water bridges: B:A.89, B:A.89 SO4.8: 2 residues within 4Å: Chain D: R.87, A.89 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.87, D:R.87 Salt bridges: D:R.87 SO4.13: 8 residues within 4Å: Chain E: H.1, E.2 Chain F: H.1, E.2, R.3, Y.5 Ligands: K.12, SO4.14 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:H.1, F:E.2, F:R.3, F:R.3, F:Y.5, E:E.2 Water bridges: F:H.1, E:R.3 Salt bridges: F:R.3 SO4.14: 2 residues within 4Å: Ligands: K.12, SO4.13 1 PLIP interactions: 1 interactions with chain E Water bridges: E:H.1

1 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.3: 6 residues within 4Å: Chain B: Y.102, W.104, D.106, S.107, P.108 Chain F: R.13 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: B:Y.102 Water bridges: E:S.4 Salt bridges: F:R.13

1 x K: POTASSIUM ION(Non-covalent)

K.12: 4 residues within 4Å: Chain E: H.1 Chain F: H.1 Ligands: SO4.13, SO4.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saphire, E.O. et al., Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope. To be Published

Release Date

2004-04-13

Peptides

IMMUNOGLOBULIN LIGHT CHAIN: AC
IMMUNOGLOBULIN HEAVY CHAIN: BD
B2.1 peptide: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
M

B
H

D
K

E
P

F
R

IMMUNOGLOBULIN LIGHT CHAIN

IMMUNOGLOBULIN HEAVY CHAIN

B2.1 peptide

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