SMTL ID : 8d0y.1

Crystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with CD4bs targeting antibody 21N13 and interface targeting antibody 35O22 at 4.7 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.70 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.1: 20 residues within 4Å: Chain A: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain B: H.93, N.94 Chain E: E.56, N.57 Chain F: G.10, S.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.33, A:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN.17: 20 residues within 4Å: Chain G: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain H: H.93, N.94 Chain K: E.56, N.57 Chain L: G.10, S.11 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:H.33, G:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN.33: 20 residues within 4Å: Chain M: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain N: H.93, N.94 Chain Q: E.56, N.57 Chain R: G.10, S.11 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:H.33, M:R.110

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.2: 8 residues within 4Å: Chain E: M.64, W.65, N.194, T.196, P.198, I.232, R.233, S.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.236 NAG-NAG.6: 4 residues within 4Å: Chain E: T.331, N.345, S.347 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 8 residues within 4Å: Chain K: M.64, W.65, N.194, T.196, P.198, I.232, R.233, S.234 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.236 NAG-NAG.22: 4 residues within 4Å: Chain K: T.331, N.345, S.347 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 8 residues within 4Å: Chain Q: M.64, W.65, N.194, T.196, P.198, I.232, R.233, S.234 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:N.236 NAG-NAG.38: 4 residues within 4Å: Chain Q: T.331, N.345, S.347 Ligands: NAG.46 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.3: 5 residues within 4Å: Chain E: H.54, K.189, D.190, K.191, N.201 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 5 residues within 4Å: Chain K: H.54, K.189, D.190, K.191, N.201 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.54 NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 5 residues within 4Å: Chain Q: H.54, K.189, D.190, K.191, N.201 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:H.54

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.4: 9 residues within 4Å: Chain E: K.33, K.34, N.222, N.336, G.338, R.392, C.393, V.394, S.395 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.33, E:K.34, E:K.34, E:G.338 NAG-NAG-BMA-MAN-MAN-MAN.20: 9 residues within 4Å: Chain K: K.33, K.34, N.222, N.336, G.338, R.392, C.393, V.394, S.395 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:K.33, K:K.34, K:K.34, K:G.338 NAG-NAG-BMA-MAN-MAN-MAN.36: 9 residues within 4Å: Chain Q: K.33, K.34, N.222, N.336, G.338, R.392, C.393, V.394, S.395 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:K.33, Q:K.34, Q:K.34, Q:G.338

12 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.5: 4 residues within 4Å: Chain E: Q.253, N.255, N.291, R.392 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 6 residues within 4Å: Chain C: E.77, Q.79 Chain E: Q.144, I.145, R.152, N.157 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.145 NAG-NAG-BMA-MAN-MAN.8: 3 residues within 4Å: Chain C: S.66, S.67 Chain E: N.322 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.67 NAG-NAG-BMA-MAN-MAN.9: 2 residues within 4Å: Chain E: N.261, I.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 4 residues within 4Å: Chain K: Q.253, N.255, N.291, R.392 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 6 residues within 4Å: Chain I: E.77, Q.79 Chain K: Q.144, I.145, R.152, N.157 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:I.145 NAG-NAG-BMA-MAN-MAN.24: 3 residues within 4Å: Chain I: S.66, S.67 Chain K: N.322 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.67 NAG-NAG-BMA-MAN-MAN.25: 2 residues within 4Å: Chain K: N.261, I.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 4 residues within 4Å: Chain Q: Q.253, N.255, N.291, R.392 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 6 residues within 4Å: Chain O: E.77, Q.79 Chain Q: Q.144, I.145, R.152, N.157 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:I.145 NAG-NAG-BMA-MAN-MAN.40: 3 residues within 4Å: Chain O: S.66, S.67 Chain Q: N.322 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:S.67 NAG-NAG-BMA-MAN-MAN.41: 2 residues within 4Å: Chain Q: N.261, I.282 No protein-ligand interaction detected (PLIP)

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.10: 5 residues within 4Å: Chain E: L.225, P.251, Q.253, V.394, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.26: 5 residues within 4Å: Chain K: L.225, P.251, Q.253, V.394, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.42: 5 residues within 4Å: Chain Q: L.225, P.251, Q.253, V.394, N.396 No protein-ligand interaction detected (PLIP)

18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.11: 4 residues within 4Å: Chain E: Q.99, S.119, N.121, K.132 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain C: D.104 Chain D: N.30 Chain E: E.235, N.236, I.237, K.242 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain E: T.257, H.289, N.291, N.359, T.363, R.392 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain E: N.351, S.352, W.354 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain E: G.313, N.314, N.315 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain F: N.94, S.96 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain K: Q.99, S.119, N.121, K.132 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain I: D.104 Chain J: N.30 Chain K: E.235, N.236, I.237, K.242 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain K: T.257, H.289, N.291, N.359, T.363, R.392 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain K: N.351, S.352, W.354 Ligands: NAG-NAG.22 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain K: G.313, N.314, N.315 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain L: N.94, S.96 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain Q: Q.99, S.119, N.121, K.132 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain O: D.104 Chain P: N.30 Chain Q: E.235, N.236, I.237, K.242 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain Q: T.257, H.289, N.291, N.359, T.363, R.392 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain Q: N.351, S.352, W.354 Ligands: NAG-NAG.38 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain Q: G.313, N.314, N.315 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain R: N.94, S.96 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xian, Y. et al., The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13. To Be Published

Release Date

2023-07-19

Peptides

35O22scFv Heavy Chain Variable: AGM
35O22scFv Light Chain Variable: BHN
PGT124 Fab Heavy Chain: CIO
PGT124 Fab Light Chain: DJP
BG505SOSIPv8 gp120: EKQ
BG505SOSIPv8 gp41: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

G
D

M
D

B
E

H
E

N
E

C
H

I
H

O
H

D
L

J
L

P
L

E
G

K
G

Q
G

F
B

L
B

R
B

35O22scFv Heavy Chain Variable

35O22scFv Light Chain Variable

PGT124 Fab Heavy Chain

PGT124 Fab Light Chain

BG505SOSIPv8 gp120

BG505SOSIPv8 gp41

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