SMTL ID : 8saw.1

CryoEM structure of DH270.UCA.G57R-CH848.10.17DT

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: 9 residues within 4Å: Chain A: N.263, I.284 Chain D: S.27, Y.32, Y.93, A.94, G.95, S.96, S.97 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.94, D:S.96 NAG-NAG-BMA.5: 9 residues within 4Å: Chain E: N.263, I.284 Chain H: S.27, Y.32, Y.93, A.94, G.95, S.96, S.97 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:A.94, H:S.96 NAG-NAG-BMA.9: 9 residues within 4Å: Chain I: N.263, I.284 Chain L: S.27, Y.32, Y.93, A.94, G.95, S.96, S.97 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:A.94, L:S.96

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: 23 residues within 4Å: Chain A: V.257, T.259, H.291, N.293, T.371, T.373 Chain C: Y.32, R.98, G.99, G.100, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain D: L.48, Y.51, E.52, K.55, P.57, S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 23 residues within 4Å: Chain E: V.257, T.259, H.291, N.293, T.371, T.373 Chain G: Y.32, R.98, G.99, G.100, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain H: L.48, Y.51, E.52, K.55, P.57, S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.10: 23 residues within 4Å: Chain I: V.257, T.259, H.291, N.293, T.371, T.373 Chain K: Y.32, R.98, G.99, G.100, W.101, S.103, Y.105, Y.106, N.113, D.115, Y.116 Chain L: L.48, Y.51, E.52, K.55, P.57, S.58 No protein-ligand interaction detected (PLIP)

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: 8 residues within 4Å: Chain A: A.104, T.105, N.116, S.118, K.131, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.404, A:R.404 NAG-NAG.7: 8 residues within 4Å: Chain E: A.104, T.105, N.116, S.118, K.131, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.404, E:R.404 NAG-NAG.11: 8 residues within 4Å: Chain I: A.104, T.105, N.116, S.118, K.131, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain I: N.400, I.401, T.402, R.404 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.404, I:R.404

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

CH848.3.D0949.10.17chim.6R.SOSIP.664 gp120A: AEI
CH848.3.D0949.10.17chim.6R.SOSIP.664 gp41: BFJ
DH270.UCA. G57R heavy chain: CGK
DH270.UCA. G57R 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

CH848.3.D0949.10.17chim.6R.SOSIP.664 gp120A

CH848.3.D0949.10.17chim.6R.SOSIP.664 gp41

DH270.UCA. G57R heavy chain

DH270.UCA. G57R light chain

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