SMTL ID : 7zf6.1

Omi-12 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.102, T.104, N.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.102, A:T.104

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: W.50, F.110 Chain B: Y.33, F.92, W.97 Ligands: CIT.6 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain A: Q.181, S.182 Chain B: Q.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.161 GOL.5: 3 residues within 4Å: Chain B: P.8, G.9, T.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.9, B:T.10, B:T.10

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: A.58, Y.60, T.69, I.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.60, A:I.70 SO4.7: 4 residues within 4Å: Chain B: K.40, Q.43, R.46 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.40, B:R.46 SO4.8: 6 residues within 4Å: Chain B: Q.38, K.40, R.46, P.60, R.62 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.40, B:E.82 Salt bridges: B:K.40, B:R.46, B:R.62 SO4.9: 3 residues within 4Å: Chain B: R.30, S.31, S.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.31, B:S.32, B:S.32 Salt bridges: B:R.30 SO4.10: 4 residues within 4Å: Chain A: P.133 Chain B: S.122, D.123, E.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.123, B:E.124 SO4.11: 4 residues within 4Å: Chain B: P.60, D.61, R.62, R.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.61, B:R.62 Salt bridges: B:R.62 SO4.12: 2 residues within 4Å: Chain B: Q.27, S.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.27, B:S.28 SO4.13: 3 residues within 4Å: Chain A: G.172, H.174 Chain B: N.139 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.172, B:N.139 SO4.14: 3 residues within 4Å: Chain B: S.115, N.138, N.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.115, B:N.138, B:N.139 SO4.15: 4 residues within 4Å: Chain B: G.93, S.94, S.95 Ligands: CIT.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.95

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 9 residues within 4Å: Chain A: W.50 Chain B: Y.33, F.92, G.93, S.94, S.95, W.97 Ligands: GOL.2, SO4.15 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.97, A:W.50 Hydrogen bonds: B:Y.33, B:F.92, B:S.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nutalai, R. et al., Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell (2022)

Release Date

2022-06-01

Peptides

Omi-12 heavy chain: A
Omi-12 light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Omi-12 heavy chain

Omi-12 light chain

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