SMTL ID : 8txp.1

Crystal structure of 05.GC.w13.01 Fab in complex with H1 HA from A/California/04/2009(H1N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain A: E.38, K.40, H.41, N.42, A.289, N.291 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: K.26, N.27 Chain G: T.101, W.102 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain E: E.38, K.40, H.41, N.42, A.289, N.291 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain E: K.26, N.27 Chain K: T.101, W.102 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain I: E.38, K.40, H.41, N.42, A.289, N.291 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: T.101, W.102 Chain I: K.26, N.27 No protein-ligand interaction detected (PLIP)

9 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: 7 residues within 4Å: Chain A: N.68, E.70, D.90, N.91, C.94, P.141, R.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.225 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: D.278, C.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: N.15 Chain C: Q.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 7 residues within 4Å: Chain E: N.68, E.70, D.90, N.91, C.94, P.141, R.225 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.225 NAG-NAG-BMA.9: 3 residues within 4Å: Chain E: D.278, C.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 2 residues within 4Å: Chain E: N.15 Chain G: Q.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 7 residues within 4Å: Chain I: N.68, E.70, D.90, N.91, C.94, P.141, R.225 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.225 NAG-NAG-BMA.14: 3 residues within 4Å: Chain I: D.278, C.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain I: N.15 Chain K: Q.65 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McIntire, K.M. et al., Maturation of germinal center B cells after influenza virus vaccination in humans. J.Exp.Med. (2024)

Release Date

2024-06-26

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
GC_w13_A, Fab heavy chain: CGK
GC_w13_A, Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

Hemagglutinin

Hemagglutinin

GC_w13_A, Fab heavy chain

GC_w13_A, Fab light chain

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