SMTL ID : 6v6w.2 (1 other biounit)

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.50 Å

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 8 residues within 4Å: Chain C: T.267, H.299, N.301, R.412 Chain D: Y.107, D.108, Y.112 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.107 NAG-NAG-BMA-MAN.16: 8 residues within 4Å: Chain I: T.267, H.299, N.301, R.412 Chain J: Y.107, D.108, Y.112 Ligands: NAG-NAG.17 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.107 NAG-NAG-BMA-MAN.31: 8 residues within 4Å: Chain O: T.267, H.299, N.301, R.412 Chain P: Y.107, D.108, Y.112 Ligands: NAG-NAG.32 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.107

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

NAG-NAG.2: 7 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 7 residues within 4Å: Chain O: Q.263, N.265, N.301, V.302, S.303, R.412 Ligands: NAG-NAG-BMA-MAN.31 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.3: 14 residues within 4Å: Chain A: N.30, F.31, Y.32, H.33, D.57, L.109, R.110, D.111, G.112, S.113, T.115 Chain C: N.58 Chain F: L.9, S.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.33, A:D.111, A:T.115 NAG-NAG-BMA-MAN-MAN.18: 14 residues within 4Å: Chain G: N.30, F.31, Y.32, H.33, D.57, L.109, R.110, D.111, G.112, S.113, T.115 Chain I: N.58 Chain L: L.9, S.17 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:H.33, G:D.111, G:T.115 NAG-NAG-BMA-MAN-MAN.33: 14 residues within 4Å: Chain M: N.30, F.31, Y.32, H.33, D.57, L.109, R.110, D.111, G.112, S.113, T.115 Chain O: N.58 Chain R: L.9, S.17 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:H.33, M:D.111, M:T.115

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

NAG.4: 8 residues within 4Å: Chain C: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG.10 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain C: T.105, N.118, Y.135 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG.7 Ligand excluded by PLIP NAG.7: 8 residues within 4Å: Chain C: E.181, V.224, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.6 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain C: N.332, S.333, S.334 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain C: N.271, I.292 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain C: T.105, N.107, D.110 Ligands: NAG.4 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain C: N.204, T.206, H.321 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain C: K.304, N.308, T.368, S.369, S.378 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain F: N.87, S.89 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain B: G.59 Chain C: N.3, L.4 Chain F: R.93, N.94 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain A: L.108, L.109, Y.119 Chain F: R.93, N.101, Q.106 Ligand excluded by PLIP NAG.19: 8 residues within 4Å: Chain I: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG.25 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain I: T.105, N.118, Y.135 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain I: N.232, P.261, N.416 Ligands: NAG.22 Ligand excluded by PLIP NAG.22: 8 residues within 4Å: Chain I: E.181, V.224, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.21 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain I: N.332, S.333, S.334 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain I: N.271, I.292 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain I: T.105, N.107, D.110 Ligands: NAG.19 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain I: N.204, T.206, H.321 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain I: K.304, N.308, T.368, S.369, S.378 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain L: N.87, S.89 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain H: G.59 Chain I: N.3, L.4 Chain L: R.93, N.94 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain G: L.108, L.109, Y.119 Chain L: R.93, N.101, Q.106 Ligand excluded by PLIP NAG.34: 8 residues within 4Å: Chain O: N.103, N.107, D.110, G.114, E.115, K.117, Y.161 Ligands: NAG.40 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain O: T.105, N.118, Y.135 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain O: N.232, P.261, N.416 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 8 residues within 4Å: Chain O: E.181, V.224, L.231, N.232, N.346, V.414, S.415 Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain O: N.332, S.333, S.334 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain O: N.271, I.292 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain O: T.105, N.107, D.110 Ligands: NAG.34 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain O: N.204, T.206, H.321 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain O: K.304, N.308, T.368, S.369, S.378 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain R: N.87, S.89 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain N: G.59 Chain O: N.3, L.4 Chain R: R.93, N.94 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain M: L.108, L.109, Y.119 Chain R: R.93, N.101, Q.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite. Sci Adv (2020)

Release Date

2020-09-23

Peptides

35O22 Fab Heavy chain: AGM
35O22 Fab Light chain: BHN
Envelope glycoprotein gp120: CIO
B11 DSS Fab heavy chain: DJP
B11 Fab light chain: EKQ
Envelope glycoprotein gp41: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

B
B

H
B

N
B

C
C

I
C

O
C

D
F

J
F

P
F

E
H

K
H

Q
H

F
K

L
K

R
K

35O22 Fab Heavy chain

35O22 Fab Light chain

Envelope glycoprotein gp120

B11 DSS Fab heavy chain

B11 Fab light chain

Envelope glycoprotein gp41

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