SMTL ID : 7mep.1

BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-6-1-1-mer

Ligands

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.1: 8 residues within 4Å: Chain C: E.213, L.263, N.264, N.378, G.380, V.446, S.447 Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain I: E.213, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 8 residues within 4Å: Chain M: E.213, V.256, L.263, N.264, G.380, V.446, S.447 Ligands: NAG-NAG.12 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:G.380, M:V.446

12 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: 4 residues within 4Å: Chain C: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: Q.295, N.297, N.333, S.335, R.444 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain C: N.138, N.150, S.152, Y.167 Chain E: V.2, Q.3, S.25, G.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.3 NAG-NAG.5: 6 residues within 4Å: Chain C: P.301, N.303 Chain F: M.31, Y.49, T.51, S.52 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:M.31 Hydrogen bonds: F:M.31, F:T.51 NAG-NAG.6: 5 residues within 4Å: Chain C: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain I: Q.295, N.297, N.333, V.334, S.335, R.444 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.411 NAG-NAG.9: 4 residues within 4Å: Chain I: V.136, N.150, Y.167, L.169 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.167 NAG-NAG.10: 5 residues within 4Å: Chain I: N.297, T.299, H.331, N.333, T.415 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain M: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain M: V.136, N.138, N.150, Y.167, L.169, D.322 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:Y.167 NAG-NAG.14: 3 residues within 4Å: Chain M: N.303, I.324, V.442 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain M: N.297, T.299, H.331, N.333, R.444 No protein-ligand interaction detected (PLIP)

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

NAG.16: 4 residues within 4Å: Chain C: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: N.278, T.280, N.281 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.387, S.389 Ligands: NAG.19 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.364, S.365 Ligands: NAG.18 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: K.234, N.236, T.238 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: R.194, N.199, T.200 Chain M: R.310 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.135 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: E.89, N.90 Chain D: G.529, S.530 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: D.232, T.242, N.243 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.340, S.394, W.396 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: S.389, N.393 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.639 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: R.54, A.55, T.56 Chain D: N.620, E.623 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: N.613, S.615, W.616 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain I: N.264, S.293, N.448 Ligands: NAG-NAG-BMA-MAN-MAN.7 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain I: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain I: N.278, T.280, N.281 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain I: N.387, S.389, R.419 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain I: N.364, S.365, G.367 Ligands: NAG.35, NAG.46 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain I: F.235, N.236, T.238, G.239, P.240 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain I: R.194, N.199 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain I: N.135 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain I: N.303, I.324, V.442 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain I: E.89, N.90 Chain J: S.530 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.243 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain I: E.270, E.271, N.291, E.292 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain I: N.340 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain I: N.356 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: S.389, N.393 Ligands: NAG.36 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain J: N.639 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain G: T.56, G.57 Chain J: N.620 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain J: N.613, S.615, W.616 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain M: Q.132, S.152, F.153, N.154 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain M: N.278, T.280, N.281 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain M: Q.295, N.297, N.333, V.334, S.335, R.444 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain M: T.374, N.387, S.389 Ligands: NAG.54 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain M: N.364, S.365, T.373 Ligands: NAG.53 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain M: N.236, T.238, S.276 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain I: R.310 Chain M: R.194, N.199, T.200 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain M: N.135 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain M: E.89, N.90 Chain N: G.529, S.530 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain M: T.242, N.243 Ligand excluded by PLIP NAG.60: 6 residues within 4Å: Chain M: E.269, E.270, E.271, N.291, E.292, K.345 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain M: K.336, N.340, W.396 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain M: K.352, N.356 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain M: S.389, N.393 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain N: N.639 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain K: T.56 Chain N: N.620 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain N: N.613, S.615, W.616 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., From structure to sequence: Antibody discovery using cryoEM. Sci Adv (2022)

Release Date

2022-01-26

Peptides

RM19R mAb Light chain: AGK
RM19R mAb Heavy chain: BHL
BG505 SOSIPv5.2(7S) - gp120: CDIJMN
Rh.33172 mAb.1 Heavy chain: E
Rh.33172 mAb.1 Light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
J

K
K

B
I

H
M

L
N

C
A

D
B

I
C

J
E

M
D

N
F

E
H

F
L

RM19R mAb Light chain

RM19R mAb Heavy chain

BG505 SOSIPv5.2(7S) - gp120

Rh.33172 mAb.1 Heavy chain

Rh.33172 mAb.1 Light chain

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