SMTL ID : 6p8m.1

Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120 core G459C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.59 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 17 residues within 4Å: Chain A: T.93, F.94, D.95, P.96, K.136, V.138, N.146, F.243, N.244, C.245, G.246, I.292, T.297, C.298, K.299, S.300, D.301 No protein-ligand interaction detected (PLIP)

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: S.207, N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.207 NAG.13: 4 residues within 4Å: Chain A: N.81, T.82, V.283 Chain B: T.30 No protein-ligand interaction detected (PLIP) NAG.14: 6 residues within 4Å: Chain A: N.114, T.116, F.117, P.122, N.124 Ligands: NAG.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.116, A:T.116, A:N.124 NAG.15: 5 residues within 4Å: Chain A: E.40, V.42, N.113, N.125 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.42 NAG.16: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, Q.212, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.154 NAG.17: 4 residues within 4Å: Chain A: K.174, S.202, R.204, N.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.202, A:N.205 NAG.18: 4 residues within 4Å: Chain A: K.218, H.223, K.224, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.218 NAG.19: 5 residues within 4Å: Chain A: L.236, T.239, T.240, N.253, S.255 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.240 Hydrogen bonds: A:N.253 NAG.20: 6 residues within 4Å: Chain A: S.227, F.228, Q.229, N.259, D.260, T.261 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.229, A:D.260 Hydrogen bonds: A:D.260, A:T.261

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 2 residues within 4Å: Chain A: K.111, H.133 No protein-ligand interaction detected (PLIP) NH4.4: 3 residues within 4Å: Chain A: G.234 Chain B: T.71 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) NH4.5: 3 residues within 4Å: Chain A: V.342, E.343, I.344 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.343 NH4.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.6: 7 residues within 4Å: Chain A: S.231, S.232, G.233, T.239 Chain B: Y.60, T.69 Ligands: NH4.4 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: D.235, L.236, N.278, K.285 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: T.80, N.81, T.82, S.83 No protein-ligand interaction detected (PLIP) PEG.21: 6 residues within 4Å: Chain B: S.120, S.121, A.122, F.154, L.178, G.182 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: Q.275, A.289, P.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.275 NA.10: 1 residues within 4Å: Chain A: K.274 No protein-ligand interaction detected (PLIP) NA.11: 2 residues within 4Å: Chain A: K.78, L.85 No protein-ligand interaction detected (PLIP) NA.22: 4 residues within 4Å: Chain B: S.88, T.91, V.119, S.120 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: V.139, S.242, F.243, F.249 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parks, K.R. et al., Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization. Cell Rep (2019)

Release Date

2019-11-20

Peptides

Gp120: A
P-p3b3 Heavy Chain: B
P-p3b3 Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

Gp120

P-p3b3 Heavy Chain

P-p3b3 Light Chain