SMTL ID : 6um5.1

Cryo-EM structure of HIV-1 neutralizing antibody DH270 UCA3 in complex with CH848 10.17DT Env

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: T.104, N.115, Y.132, L.134, D.281 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: R.153, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.195, S.235 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain E: T.104, N.115, Y.132, L.134, D.281 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain E: R.153, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: N.195, S.235 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain I: T.104, N.115, Y.132, L.134, D.281 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain I: R.153, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain I: N.195, S.235 Ligands: NAG.45 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- BMA- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-beta-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-BMA-MAN.2: 14 residues within 4Å: Chain A: H.290, N.292, T.372 Chain C: Y.32, R.98, W.101, S.103, Y.106, Y.111, N.113, D.115 Chain D: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.32 NAG-NAG-BMA-MAN-MAN-BMA-MAN.9: 14 residues within 4Å: Chain E: H.290, N.292, T.372 Chain G: Y.32, R.98, W.101, S.103, Y.106, Y.111, N.113, D.115 Chain H: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.32 NAG-NAG-BMA-MAN-MAN-BMA-MAN.16: 14 residues within 4Å: Chain I: H.290, N.292, T.372 Chain K: Y.32, R.98, W.101, S.103, Y.106, Y.111, N.113, D.115 Chain L: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.32

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

NAG-NAG-BMA-NAG.3: 8 residues within 4Å: Chain A: N.261, N.262, N.263 Chain D: Q.1, Y.32, Y.93, G.95, S.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.1 NAG-NAG-BMA-NAG.10: 8 residues within 4Å: Chain E: N.261, N.262, N.263 Chain H: Q.1, Y.32, Y.93, G.95, S.96 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.1 NAG-NAG-BMA-NAG.17: 8 residues within 4Å: Chain I: N.261, N.262, N.263 Chain L: Q.1, Y.32, Y.93, G.95, S.96 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.1

6 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.4: 2 residues within 4Å: Chain A: N.399 Chain D: Y.32 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.32 NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: N.299, Q.303, N.351, T.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain E: N.399 Chain H: Y.32 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:Y.32 NAG-NAG-BMA.13: 4 residues within 4Å: Chain E: N.299, Q.303, N.351, T.361 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 2 residues within 4Å: Chain I: N.399 Chain L: Y.32 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:Y.32 NAG-NAG-BMA.20: 4 residues within 4Å: Chain I: N.299, Q.303, N.351, T.361 No protein-ligand interaction detected (PLIP)

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

NAG.22: 3 residues within 4Å: Chain A: N.223, R.403 Ligands: NAG.30 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: Q.322, N.345, S.347 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.351 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.119, E.128 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: K.319, N.321 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.237 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: G.56, N.57 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.190, N.202 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: P.252, N.405 Ligands: NAG.22 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: N.223, R.403 Ligands: NAG.39 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: Q.322, N.345, S.347 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain E: N.351 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: N.119, E.128 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: K.319, N.321 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.237 Ligands: NAG-NAG.14 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: G.56, N.57 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: N.190, N.202 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: P.252, N.405 Ligands: NAG.31 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain I: N.223, R.403 Ligands: NAG.48 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain I: Q.322, N.345, S.347 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.351 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain I: N.119, E.128 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain I: K.319, N.321 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain I: N.237 Ligands: NAG-NAG.21 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain I: G.56, N.57 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: N.190, N.202 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain I: P.252, N.405 Ligands: NAG.40 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 10.17 DT gp120: AEI
Envelope glycoprotein gp160: BFJ
DH270 UCA3 Fab Heavy Chain: CGK
DH270 UCA3 Fab 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 10.17 DT gp120

Envelope glycoprotein gp160

DH270 UCA3 Fab Heavy Chain

DH270 UCA3 Fab Light Chain

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