SMTL ID : 8saq.1

CryoEM structure of DH270.6-CH848.0526.25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 7 residues within 4Å: Chain A: N.280, I.301 Chain C: Y.110 Chain D: Y.27, F.93, G.95, S.96 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.27, D:S.96 NAG-NAG-BMA.3: 7 residues within 4Å: Chain E: N.280, I.301 Chain G: Y.110 Chain H: Y.27, F.93, G.95, S.96 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.27, H:S.96 NAG-NAG-BMA.5: 7 residues within 4Å: Chain I: N.280, I.301 Chain K: Y.110 Chain L: Y.27, F.93, G.95, S.96 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Y.27, L:S.96

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-MAN-MAN.2: 15 residues within 4Å: Chain A: T.276, H.308, N.310, T.386, T.388 Chain C: W.101, S.103, Y.105, Y.106, N.113, D.115 Chain D: Y.48, Y.51, K.55, S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 15 residues within 4Å: Chain E: T.276, H.308, N.310, T.386, T.388 Chain G: W.101, S.103, Y.105, Y.106, N.113, D.115 Chain H: Y.48, Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 15 residues within 4Å: Chain I: T.276, H.308, N.310, T.386, T.388 Chain K: W.101, S.103, Y.105, Y.106, N.113, D.115 Chain L: Y.48, Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.103

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

NAG.7: 2 residues within 4Å: Chain A: N.133, Y.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.133 NAG.8: 2 residues within 4Å: Chain A: N.415, T.417 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain E: N.133, Y.150 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.133 NAG.10: 2 residues within 4Å: Chain E: N.415, T.417 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.417 NAG.11: 2 residues within 4Å: Chain I: N.133, Y.150 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.133 NAG.12: 2 residues within 4Å: Chain I: N.415, T.417 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, R. et al., Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Nat Commun (2023)

Release Date

2023-04-19

Peptides

CH848.0526.25 gp120: AEI
CH848.0526.25 gp41: BFJ
DH270.6 variable heavy chain: CGK
DH270.6 variable light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
K

B
B

F
F

J
L

C
C

G
H

K
M

D
D

H
I

L
N

CH848.0526.25 gp120

CH848.0526.25 gp41

DH270.6 variable heavy chain

DH270.6 variable light chain

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