SMTL ID : 6b3d.1

Crystal structure of anti-HIV antibody PGT128 in complex with a bacterially derived synthetic mimetic of Man9.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: V.89, G.90, N.91, W.92, D.93 Chain B: W.60, N.61, W.64, T.65, Y.66, H.67, P.69, K.72, W.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.91, A:W.92, A:W.92, A:D.93

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: P.8, S.9, A.142, V.143, T.144, T.195, H.196, E.197 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.9, A:A.142, A:T.144, A:E.197, A:E.197, A:E.197 Water bridges: A:V.143, A:V.143 GOL.3: 3 residues within 4Å: Chain A: G.106, Q.107, P.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.106 GOL.4: 7 residues within 4Å: Chain A: T.77, E.80, T.103, V.104, Y.139, K.165, Y.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.80, A:K.165, A:K.165, A:Y.171

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: K.148, D.150, S.151, S.189, S.191, E.202, T.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.148, A:K.148, A:S.189, A:S.191 EDO.6: 5 residues within 4Å: Chain A: Q.35, H.36, A.37, G.38, K.39 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.41, B:G.44 Hydrogen bonds: A:G.38, A:K.39 EDO.7: 3 residues within 4Å: Chain A: I.95, F.96 Chain B: L.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.96, A:F.96 EDO.8: 4 residues within 4Å: Chain A: P.8, V.82, G.98, G.99 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain B: P.169, E.170, Y.198 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.10, B:T.132, B:E.170, B:Y.198, B:Y.198 Water bridges: B:T.132 EDO.12: 3 residues within 4Å: Chain A: Y.46 Chain B: W.121, D.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.121, B:D.123

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

IPA.9: 6 residues within 4Å: Chain A: T.160, T.161, T.162 Chain B: P.43, G.44, A.190 No protein-ligand interaction detected (PLIP) IPA.13: 4 residues within 4Å: Chain B: N.177, A.180, L.181, Q.214 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.180, B:L.181 Hydrogen bonds: B:N.177 IPA.14: 3 residues within 4Å: Chain B: L.111, R.112, Y.113 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.112 Hydrogen bonds: B:Y.113

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 6 residues within 4Å: Chain B: H.55, R.62, T.65, H.67, T.76, L.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.77 Salt bridges: B:H.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pantophlet, R. et al., Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity. Nat Commun (2017)

Release Date

2017-12-06

Peptides

PGT128 Fab light chain: A
PGT128 Fab heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

PGT128 Fab light chain

PGT128 Fab heavy chain

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