SMTL ID : 8e1p.1

Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.82 Å

Oligo State

hetero-3-1-2-3-3-3-3-mer

Ligands

4 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.1: 7 residues within 4Å: Chain I: E.174, V.217, N.225, N.339, C.406, V.407, S.408 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 8 residues within 4Å: Chain J: L.224, N.225, N.339, G.341, C.406, V.407, S.408 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain J: P.254, N.409 Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 6 residues within 4Å: Chain L: N.225, N.339, R.405, V.407, S.408 Ligands: NAG.40 No protein-ligand interaction detected (PLIP)

9 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: 3 residues within 4Å: Chain I: N.264, I.285, V.403 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain I: N.325, S.326, T.334 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain I: G.226, L.228, P.254, N.409, T.411 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain J: Q.256, N.258, V.295, S.296, R.405 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain J: N.264, I.285, V.403 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain J: N.325, S.326, D.348, S.350 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain L: V.104, N.118, S.120, H.135 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain L: N.264, I.285, V.403 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain L: N.325 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.3: 17 residues within 4Å: Chain H: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain I: T.260, H.292, N.294, T.376 Chain N: R.103, I.104, G.106, V.107 Ligands: NAG.22 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-MAN-MAN-MAN-MAN-MAN-MAN.9: 17 residues within 4Å: Chain G: N.45, N.46, Q.47, D.48, P.61, D.62 Chain J: N.258, T.260, H.292, N.294, T.376 Chain M: R.103, I.104, Y.105, G.106, V.107, V.108 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: 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.15: 8 residues within 4Å: Chain L: T.260, H.292, N.294 Chain O: I.104, G.106, V.107 Ligands: MAN-MAN-MAN.16, MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP)

1 x MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose

MAN-MAN-MAN.16: 10 residues within 4Å: Chain K: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain O: R.103 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.15 No protein-ligand interaction detected (PLIP)

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

NAG.18: 3 residues within 4Å: Chain I: N.103, G.114, K.140 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain I: N.118, S.120, H.135, D.283 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain I: N.122, R.131, K.133 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain I: N.197, T.199, P.201, I.240 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain I: Q.256, N.258, N.294, R.405 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain I: K.297, N.301 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain I: R.312, K.313, N.317 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain I: N.354 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain J: E.57, N.58 Chain P: S.17 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain J: N.118, H.135, L.137, D.283 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain J: T.98, N.122 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain J: N.197, T.199 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain J: N.301 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain J: N.317 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain J: N.354 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain L: E.57, N.58 Chain R: G.13, G.16, S.17 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain L: N.103, K.140 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain L: T.98, S.120, F.121, N.122 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain L: W.66, N.197, G.198, T.199, S.237 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain L: Q.256, N.258, N.294, R.405 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain L: K.297, N.301 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain L: N.354 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain L: N.225, L.228, P.254, N.409 Ligands: NAG-NAG-BMA.13 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain P: N.100, S.102 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain P: N.107, E.110 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain P: E.123, N.126 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain Q: N.100 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain Q: N.126 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain R: N.100, S.102 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain R: N.105, N.107, E.110 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caniels, T.G. et al., Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions. Cell Rep Med (2023)

Release Date

2023-06-21

Peptides

germline PGV20 heavy chain: ABE
germline PGV20 light chain: C
germline PGV20 light chain: DF
PGT124 Fab Light Chain: GHK
BG505-SOSIP.v4.1-GT1.2gp120: IJL
PGT124 Fab Heavy Chain: MNO
Envelope glycoprotein gp41: PQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
H

E
N

C
I

D
L

F
O

G
A

H
C

K
J

I
E

J
G

L
M

M
B

N
D

O
K

P
Y

Q
X

R
Z

germline PGV20 heavy chain

germline PGV20 light chain

germline PGV20 light chain

PGT124 Fab Light Chain

BG505-SOSIP.v4.1-GT1.2gp120

PGT124 Fab Heavy Chain

Envelope glycoprotein gp41

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