SMTL ID : 7t9b.1

ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-1-1-mer

Ligands

10 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: Q.324, T.333, T.334, N.347, S.349 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.257, T.259, H.291, N.293 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 Chain M: Y.115 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain E: Q.324, T.333, T.334, N.347, S.349 Ligands: NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.257, T.259, H.291, N.293, T.375 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain E: V.104, T.105, N.118, S.120, Y.135, D.282 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.135 NAG-NAG.15: 6 residues within 4Å: Chain I: Q.324, T.333, T.334, N.347, S.349 Ligands: NAG.56 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.324 NAG-NAG.16: 6 residues within 4Å: Chain I: N.257, T.259, H.291, N.293, T.375, R.404 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain A: R.270 Chain I: V.144, M.146, N.159 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain I: V.104, T.105, N.118, Y.135, L.137, D.282 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135

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.3: 11 residues within 4Å: Chain A: N.37, S.171, P.174, V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 11 residues within 4Å: Chain E: S.171, E.173, P.174, V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.45 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.171, E:S.171 NAG-NAG-BMA-MAN.17: 10 residues within 4Å: Chain I: S.171, P.174, V.216, L.223, N.224, N.338, G.340, V.406, S.407 Ligands: NAG.59 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.340

2 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.4: 11 residues within 4Å: Chain A: V.104, T.105, N.118, Y.135, L.137, K.267, D.282 Chain M: K.54, T.55, E.56, G.57 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain A Hydrogen bonds: M:T.55, M:T.55, A:K.267, M:G.57 Hydrophobic interactions: A:Y.135 NAG-NAG-BMA.20: 13 residues within 4Å: Chain I: T.98, S.120, F.121, N.122, R.131, W.150, T.151 Chain M: D.106, D.117, Y.119, R.121 Chain N: T.57, G.58 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain I Hydrophobic interactions: M:Y.119 Hydrogen bonds: M:Y.119, I:W.150

1 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-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 22 residues within 4Å: Chain A: T.98, Q.100, S.120, N.122 Chain E: N.129 Chain M: R.50, T.100, G.101, E.103, Y.105, Y.118, F.120, D.122 Chain N: I.32, Y.33, Y.37, L.47, Y.50, G.51, S.53, S.54, Y.92 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:E.103, M:Y.118, N:S.54, N:S.54, N:S.53, N:S.53

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.6: 4 residues within 4Å: Chain B: N.107, S.109, E.110 Chain C: S.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.109, B:S.109 NAG-FUC.13: 5 residues within 4Å: Chain F: N.105, R.106, N.107, E.110 Ligands: NAG.50 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.105, F:N.107, F:N.107 NAG-FUC.21: 5 residues within 4Å: Chain J: N.105, N.107, S.109, E.110 Chain K: S.107 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.105

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.7: 5 residues within 4Å: Chain B: N.100, S.102, W.103, Y.127, I.130 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.127 Hydrogen bonds: B:S.102 NAG-NAG-FUC.14: 5 residues within 4Å: Chain F: N.100, S.102, W.103, Y.127, I.130 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.127 Hydrogen bonds: F:S.102 NAG-NAG-FUC.22: 5 residues within 4Å: Chain J: N.100, S.102, W.103, Y.127, I.130 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.127

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

NAG.23: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.196, I.234, S.236, H.313 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.316 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.238, N.241 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: Q.324, S.349, N.353 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: K.296, N.300, W.356 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: Q.255, N.257, N.293, S.295 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: N.224, P.253, N.408 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.263, I.284, V.402 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: R.154, N.159, T.160 Chain E: R.270 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.103, K.117 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.196, T.198, S.236, H.313 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.107 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.316 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.238, T.240, N.241 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: S.349, N.353 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: K.296, N.300, W.356 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain E: Q.255, N.257, N.293, S.295, R.404 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain E: N.224, V.406, S.407, N.408 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.263, I.284, V.402 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain E: V.144, R.154, N.159, T.160 Chain I: R.270 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: N.103, R.113, W.150 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain F: K.122, E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain F: S.109, E.110, D.113, N.114 Ligands: NAG-FUC.13 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain I: E.57, N.58 Chain J: G.16, S.17 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain I: N.196, T.198, S.236, H.313 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain I: N.106, N.107 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain I: N.316 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain I: N.238, T.240, N.241 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain I: Q.324, S.349, N.353 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain I: N.300, W.356 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain I: Q.255, N.257, N.293, S.295, R.404 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain I: N.224, V.406, S.407, N.408 Ligands: NAG-NAG-BMA-MAN.17 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain I: N.263, I.284, V.402 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain I: N.103, R.113, G.114 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain J: S.109, E.110, N.114 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melzi, E. et al., Priming HIV Envelope V2 Apex-directed broadly neutralizing antibody responses with protein or mRNA immunogens. Immunity (2022)

Release Date

2022-09-28

Peptides

HIV-1 Envelope ApexGT5 gp120: AEI
HIV-1 Envelope ApexGT5 gp41: BFJ
RM20A3 Fab Heavy Chain: CGK
RM20A3 Fab Light Chain: DHL
GT5-d42.16 Fab Heavy Chain: M
GT5-d42.16 Fab Light Chain: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
E

B
B

F
D

J
F

C
J

G
M

K
O

D
K

H
N

L
P

M
H

N
L

HIV-1 Envelope ApexGT5 gp120

HIV-1 Envelope ApexGT5 gp41

RM20A3 Fab Heavy Chain

RM20A3 Fab Light Chain

GT5-d42.16 Fab Heavy Chain

GT5-d42.16 Fab Light Chain

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