SMTL ID : 7ucg.1

Structure of the DU422 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

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

Ligands

21 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: 5 residues within 4Å: Chain C: Q.16, S.17, N.19, S.68, T.70 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.19, C:S.68, C:S.68 NAG-NAG.2: 4 residues within 4Å: Chain I: Q.16, S.17, N.19, T.70 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.19, I:N.19 NAG-NAG.3: 4 residues within 4Å: Chain O: Q.16, S.17, N.19, S.68 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain D: N.161, Y.178 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain D: V.90, N.238, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain C: Y.26, L.29, E.46, V.47 Chain D: N.285 Ligands: NAG.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.29, C:V.47 NAG-NAG.8: 5 residues within 4Å: Chain D: N.304, N.340, S.342, T.413, K.446 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: N.310, T.312, I.331 Chain F: F.65 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:F.65 NAG-NAG.11: 2 residues within 4Å: Chain D: N.392, T.394 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain J: N.161, Y.178 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.178 NAG-NAG.13: 3 residues within 4Å: Chain J: V.90, N.238, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain I: Y.26, L.29, E.46, V.47 Chain J: N.285 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.29, I:V.47 NAG-NAG.16: 6 residues within 4Å: Chain J: E.302, N.304, N.340, S.342, T.413, K.446 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain J: N.310, I.331 Chain L: F.65 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:F.65 NAG-NAG.19: 2 residues within 4Å: Chain J: N.392, T.394 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain P: N.161, Y.178 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain P: V.90, N.238, N.250 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain O: Y.26, L.29, E.46, V.47 Chain P: N.285 Ligands: NAG.48 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:V.47 NAG-NAG.24: 5 residues within 4Å: Chain P: E.302, N.304, N.340, S.342, K.446 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain P: N.310, T.312, I.331 Chain R: F.65 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:F.65 NAG-NAG.27: 2 residues within 4Å: Chain P: N.392, T.394 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.6: 13 residues within 4Å: Chain D: E.69, R.71, D.220, P.221, V.263, L.270, N.271, N.383, R.385, C.445, K.446 Chain N: Q.1 Ligands: NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 11 residues within 4Å: Chain B: Q.1 Chain J: R.71, D.220, P.221, L.270, N.271, N.383, R.385, C.445, K.446 Ligands: NAG.41 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:D.220 NAG-NAG-BMA-MAN-MAN.22: 12 residues within 4Å: Chain H: Q.1 Chain P: R.71, D.220, P.221, V.263, L.270, N.271, N.383, R.385, C.445, K.446 Ligands: NAG.47 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain H Hydrogen bonds: P:D.220, H:Q.1

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.10: 18 residues within 4Å: Chain D: N.304, T.306, H.338, N.340, T.413, I.415 Chain E: R.103, I.104, G.106, V.107, V.108 Chain F: S.25, N.45, N.46, Q.47, D.62, I.63, N.64 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 19 residues within 4Å: Chain J: N.304, T.306, H.338, N.340, T.413, I.415 Chain K: R.103, I.104, G.106, V.107, V.108 Chain L: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 18 residues within 4Å: Chain P: N.304, T.306, H.338, N.340, T.413, I.415 Chain Q: R.103, I.104, G.106, V.107, V.108 Chain R: S.25, N.45, N.46, Q.47, D.62, I.63, N.64 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:V.108

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

NAG.28: 2 residues within 4Å: Chain A: S.17 Chain D: N.93 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: T.133, N.165 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.206 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: N.243, T.245, E.284 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: R.343, N.347, I.351 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: R.343, K.395, N.398 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain D: N.271, S.300, E.302, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.6 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: S.17 Chain J: E.92, N.93 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain J: S.163, N.165 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain J: N.206 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain J: N.243, E.284 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain J: R.343, E.344, N.347, I.351 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain J: K.395, N.398, E.399 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain J: S.300, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain M: S.17 Chain P: E.92, N.93 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain P: S.163, N.165 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain P: V.187, P.188, N.206 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain P: R.343, E.344, N.347, I.351 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain P: K.395, N.398, E.399 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain P: N.271, E.302, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.22 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain P: N.243, G.244, T.245, S.283 Ligands: NAG-NAG.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. Sci Adv (2022)

Release Date

2022-08-17

Peptides

Envelope glycoprotein gp41: AGM
BG24 CDRH2-v2 Fab heavy chain: BHN
BG24 light chain: CIO
Envelope glycoprotein gp160: DJP
10-1074 Fab heavy chain: EKQ
10-1074 light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
A

M
M

B
D

H
C

N
N

C
E

I
F

O
O

D
G

J
I

P
P

E
H

K
J

Q
Q

F
L

L
K

R
R

Envelope glycoprotein gp41

BG24 CDRH2-v2 Fab heavy chain

BG24 light chain

Envelope glycoprotein gp160

10-1074 Fab heavy chain

10-1074 light chain

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