SMTL ID : 7pc2.1

HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 and the antibody 3BNC117.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

19 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: 4 residues within 4Å: Chain G: E.57, N.58 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain G: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain G: N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain G: R.162, N.167 Chain M: H.73, W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain H: E.57, N.58 Chain L: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain H: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain H: N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain H: R.162, N.167, T.168 Chain O: H.73, S.75, W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain H: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain I: N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain I: R.162, N.167, T.168 Chain N: W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 5 residues within 4Å: Chain I: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain P: T.20, R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 5 residues within 4Å: Chain Q: T.20, R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 5 residues within 4Å: Chain R: T.20, R.61, W.63, E.66, N.68 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.5: 11 residues within 4Å: Chain E: R.31, D.104 Chain G: E.181, L.231, N.232, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.27: 11 residues within 4Å: Chain A: R.31, D.104 Chain H: E.181, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.24 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:V.414 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.33: 12 residues within 4Å: Chain C: R.31, D.104 Chain I: E.181, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.39 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.414

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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.6: 9 residues within 4Å: Chain G: N.246 Chain P: G.27, Y.28, R.62, W.63, G.64, Q.65, Y.67, Y.87 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.28 Hydrogen bonds: P:R.62, P:R.62, P:Q.65 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20: 8 residues within 4Å: Chain H: N.246 Chain R: G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 3 PLIP interactions: 3 interactions with chain R Hydrophobic interactions: R:Y.28 Hydrogen bonds: R:R.62, R:R.62 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.34: 10 residues within 4Å: Chain I: N.246 Chain Q: G.27, Y.28, R.62, W.63, G.64, Q.65, Y.67, Y.87 Ligands: NAG.56 2 PLIP interactions: 2 interactions with chain Q Hydrophobic interactions: Q:Y.28 Hydrogen bonds: Q:R.62, Q:R.62, Q:R.62, Q:R.62

10 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.7: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG-BMA.11, NAG-NAG-BMA-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 1 residues within 4Å: Chain H: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN.22, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 3 residues within 4Å: Chain H: S.357, N.361 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 4 residues within 4Å: Chain I: E.57, N.58 Chain K: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 1 residues within 4Å: Chain I: N.271 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 6 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.36, NAG-NAG-BMA-MAN-MAN.36, NAG-NAG-BMA-MAN-MAN.36, NAG-NAG-BMA.38 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 3 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN.9: 23 residues within 4Å: Chain E: M.2, F.27, R.31, F.32, K.98, D.99, D.100, I.101, L.102, Y.115, Q.117, D.120 Chain F: R.45, V.46, A.56, T.57 Chain G: N.107, T.109, D.110, T.267, D.294, H.299, N.301 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:Q.117, E:Q.117, F:R.45, F:V.46, F:V.46, F:A.56, F:T.57, F:T.57, E:D.120 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 22 residues within 4Å: Chain A: M.2, F.27, R.31, F.32, K.98, D.100, I.101, L.102, Y.115, Q.117, D.120 Chain B: R.45, V.46, A.56, T.57 Chain H: N.107, T.109, D.110, T.267, D.294, H.299, N.301 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.117, A:Q.117, B:R.45, B:V.46, B:V.46, B:T.57, A:D.120 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.41: 22 residues within 4Å: Chain C: M.2, F.27, R.31, F.32, K.98, D.100, I.101, L.102, Y.115, Q.117, D.120 Chain D: R.45, V.46, A.56, T.57 Chain I: N.107, T.109, D.110, T.267, D.294, H.299, N.301 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.117, C:Q.117, D:R.45, D:V.46, D:V.46, D:T.57, C:D.120

1 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-(1-3)]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.10: 13 residues within 4Å: Chain E: D.57, Y.59, T.107, S.108, Y.111, W.112, Y.114, Y.115 Chain F: N.93, W.94 Chain G: Q.263, N.265, S.303 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.107, E:S.108, E:Y.111

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.13: 5 residues within 4Å: Chain G: N.332, S.333, N.355 Ligands: NAG-NAG-BMA.14, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 7 residues within 4Å: Chain H: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.36: 6 residues within 4Å: Chain I: N.332, S.333, T.341, N.355 Ligands: NAG-NAG-BMA.37, NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN.25: 14 residues within 4Å: Chain A: D.57, Y.59, T.107, S.108, H.109, Y.111, W.112, Y.114, Y.115 Chain B: N.93, W.94 Chain H: Q.263, N.265, S.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.107, A:S.108, A:Y.111 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.40: 14 residues within 4Å: Chain C: D.57, Y.59, T.107, S.108, H.109, Y.111, W.112, Y.114, Y.115 Chain D: N.93, W.94 Chain I: Q.263, N.265 Ligands: NAG.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.107, C:S.108, C:Y.111

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

NAG.45: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: S.67 Chain G: S.378, N.379 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.107 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain G: N.204 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain H: N.204 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain H: N.308, W.364 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: S.67 Chain H: S.378, N.379 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain H: N.106, N.107 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain I: N.204 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.34 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain I: N.308, W.364 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain D: S.67 Chain I: N.379 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.40 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain J: N.126, Y.127 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain K: N.100, S.102 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain K: N.126 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain L: N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorin, V. et al., Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller. J.Exp.Med. (2022)

Release Date

2022-02-23

Peptides

7-269 IgA Fab heavy chain: ACE
7-269 IgA Fab light chain: BDF
gp120, BG505 SOSIP.664 T332N: GHI
gp41 BG505 T332N SOSIP.664: JKL
3BNC IgG Fab heavy chain: MNO
3BNC117 IgG Fab light chain: PQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
M

E
Q

B
P

D
N

F
R

G
A

H
B

I
C

J
D

K
E

L
F

M
K

N
G

O
I

P
L

Q
H

R
J

7-269 IgA Fab heavy chain

7-269 IgA Fab light chain

gp120, BG505 SOSIP.664 T332N

gp41 BG505 T332N SOSIP.664

3BNC IgG Fab heavy chain

3BNC117 IgG Fab light chain

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