SMTL ID : 8sax.1

CryoEM structure of DH270.UCA-CH848.10.17DT

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 7 residues within 4Å: Chain A: N.263, I.284 Chain D: D.28, Y.93, A.94, G.95, S.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.27, D:D.28, D:A.94 NAG-NAG-BMA-MAN.5: 9 residues within 4Å: Chain E: N.263, I.284 Chain H: T.25, S.27, D.28, Y.93, A.94, G.95, S.96 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.27, H:D.28, H:A.94 NAG-NAG-BMA-MAN.9: 8 residues within 4Å: Chain I: N.263, I.284 Chain L: T.25, D.28, Y.93, A.94, G.95, S.96 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.28, L:A.94

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.2: 16 residues within 4Å: Chain A: H.291, N.293, T.371, T.373 Chain C: Y.32, R.98, G.99, W.101, S.103, Y.106, N.113, D.115, Y.116 Chain D: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.32, C:W.101 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 16 residues within 4Å: Chain E: H.291, N.293, T.371, T.373 Chain G: Y.32, R.98, G.99, W.101, S.103, Y.106, N.113, D.115, Y.116 Chain H: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.32, G:W.101 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.10: 16 residues within 4Å: Chain I: H.291, N.293, T.371, T.373 Chain K: Y.32, R.98, G.99, W.101, S.103, Y.106, N.113, D.115, Y.116 Chain L: Y.51, K.55, S.58 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.32, K:W.101

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

NAG-NAG.3: 3 residues within 4Å: Chain A: N.116, S.118, Y.133 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain E: N.116, S.118, Y.133 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain E: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain I: N.116, S.118, Y.133 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain I: N.400, T.402 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

CH848.10.17.SOSIP gp120: AEI
CH848.10.17.SOSIP gp41: BFJ
DH270.UCA heavy chain: CGK
DH270.UCA 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.SOSIP gp120

CH848.10.17.SOSIP gp41

DH270.UCA heavy chain

DH270.UCA light chain

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