SMTL ID : 6um6.1

Cryo-EM structure of HIV-1 neutralizing antibody DH270.6 in complex with CH848 10.17DT Env

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 8 residues within 4Å: Chain A: H.291, N.293, T.371, T.373 Chain C: W.101, S.103, Y.105, Y.106 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.101, C:Y.105 NAG-NAG-BMA-MAN.6: 8 residues within 4Å: Chain E: H.291, N.293, T.371, T.373 Chain G: W.101, S.103, Y.105, Y.106 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:W.101, G:Y.105 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain I: H.291, N.293, T.371, T.373 Chain K: W.101, S.103, Y.105, Y.106 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:W.101, K:Y.105

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.400 Chain D: H.32, D.33 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain E: N.400 Chain H: H.32, D.33 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain I: N.400 Chain L: H.32, D.33 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.263 Chain D: Y.27, G.95, S.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.27 NAG-NAG-BMA.8: 4 residues within 4Å: Chain E: N.263 Chain H: Y.27, G.95, S.96 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.27 NAG-NAG-BMA.13: 4 residues within 4Å: Chain I: N.263 Chain L: Y.27, G.95, S.96 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.27

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain A: N.322, N.352, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain E: N.322, N.352, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain I: N.322, N.352, R.427 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.5: 6 residues within 4Å: Chain A: E.173, L.223, N.224, N.337, R.404, S.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.173 NAG-NAG-BMA-MAN.10: 6 residues within 4Å: Chain E: E.173, L.223, N.224, N.337, R.404, S.405 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.173 NAG-NAG-BMA-MAN.15: 6 residues within 4Å: Chain I: E.173, L.223, N.224, N.337, R.404, S.405 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.173

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

NAG.16: 2 residues within 4Å: Chain A: N.116, Y.133 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.346, S.348 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: R.154, N.159, T.160 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.316 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.406 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: T.194, N.196 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain E: N.116, Y.133 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain E: N.346, S.348 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: R.154, N.159, T.160 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain E: N.316 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain E: N.406 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: T.194, N.196 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain I: N.116, Y.133 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain I: N.346, S.348 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain I: R.154, N.159, T.160 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain I: N.316 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain I: N.406 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain I: T.194, N.196 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saunders, K.O. et al., Targeted selection of HIV-specific antibody mutations by engineering B cell maturation. Science (2019)

Release Date

2019-12-18

Peptides

CH848 10.17DT gp120: AEI
CH848 10.17DT gp41: BFJ
DH270.6 Heavy chain: CGK
DH270.6 Light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

CH848 10.17DT gp120

CH848 10.17DT gp41

DH270.6 Heavy chain

DH270.6 Light chain

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