SMTL ID : 6vi0.1

Cryo-EM structure of VRC01.23 in complex with HIV-1 Env BG505 DS.SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 3 residues within 4Å: Chain B: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: Q.263, N.265, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain F: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain F: Q.263, N.265, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain F: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain J: Q.100, S.120, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain J: Q.263, N.265, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain J: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.2: 5 residues within 4Å: Chain B: R.162, N.167 Chain D: R.19, Q.73, Q.76 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.73, D:R.19 NAG-NAG-BMA-MAN.10: 5 residues within 4Å: Chain F: R.162, N.167 Chain H: R.19, Q.73, Q.76 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.73, H:R.19 NAG-NAG-BMA-MAN.18: 5 residues within 4Å: Chain J: R.162, N.167 Chain L: R.19, Q.73, Q.76 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:Q.73, L:R.19

3 x NAG- NAG- BMA- MAN- MAN- MAN: 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.3: 12 residues within 4Å: Chain B: K.35, S.179, E.181, V.224, L.231, N.232, G.348, Q.408, R.412, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.11: 12 residues within 4Å: Chain F: K.35, S.179, E.181, V.224, L.231, N.232, G.348, Q.408, R.412, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.19: 12 residues within 4Å: Chain J: K.35, S.179, E.181, V.224, L.231, N.232, G.348, Q.408, R.412, C.413, V.414, S.415 No protein-ligand interaction detected (PLIP)

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.4: 9 residues within 4Å: Chain B: N.246 Chain C: Y.25, G.26, R.61, W.62, G.63, P.64, Y.66, Y.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.61, C:R.61, C:R.61 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.12: 9 residues within 4Å: Chain F: N.246 Chain G: Y.25, G.26, R.61, W.62, G.63, P.64, Y.66, Y.86 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.61, G:R.61, G:R.61 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20: 9 residues within 4Å: Chain J: N.246 Chain K: Y.25, G.26, R.61, W.62, G.63, P.64, Y.66, Y.86 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.61, K:R.61, K:R.61

3 x NAG- NAG- BMA- MAN- MAN- MAN: 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.6: 8 residues within 4Å: Chain B: N.332, S.333, T.341, N.355, S.357 Chain D: R.91 Ligands: NAG-NAG-BMA.7, NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.14: 8 residues within 4Å: Chain F: N.332, S.333, T.341, N.355, S.357 Chain H: R.91 Ligands: NAG-NAG-BMA.15, NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.22: 8 residues within 4Å: Chain J: N.332, S.333, T.341, N.355, S.357 Chain L: R.91 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP)

3 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: 4 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 4 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.22, NAG-NAG-BMA-MAN-MAN-MAN.22 No protein-ligand interaction detected (PLIP)

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

NAG.25: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: S.17 Chain B: N.58 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.103, G.114 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: V.104, N.106, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.204 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.271, I.292, V.410 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.308 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.324 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.361 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: I.17, S.60, R.61, W.62, N.67 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: N.100, S.102 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.126 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain E: S.17 Chain F: N.58 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain F: N.103, G.114 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain F: V.104, N.106, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain F: N.204 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain F: N.271, I.292, V.410 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain F: H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain F: N.308 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain F: N.361 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain G: I.17, S.60, R.61, W.62, N.67 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain I: N.100, S.102 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain I: N.126 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain I: S.17 Chain J: N.58 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain J: N.103, G.114 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain J: V.104, N.106, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain J: N.204 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain J: N.271, I.292, V.410 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain J: H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain J: N.308 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain J: N.324 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain J: N.361 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain K: I.17, S.60, R.61, W.62, N.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, Y.D. et al., A matrix of structure-based designs yields improved VRC01-class antibodies for HIV-1 therapy and prevention. Mabs

Release Date

2021-01-13

Peptides

Envelope glycoprotein gp41: AEI
BG505 gp120: BFJ
VRC01.23 Light chain: CGK
VRC01.23 Heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E
A

I
F

B
G

F
C

J
I

C
L

G
D

K
J

D
H

H
E

L
K

Envelope glycoprotein gp41

BG505 gp120

VRC01.23 Light chain

VRC01.23 Heavy chain

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