SMTL ID : 6e5p.1

Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

9 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN-MAN.1: 10 residues within 4Å: Chain A: G.92 Chain B: A.31, H.32, T.33, K.99, G.100, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.31, B:T.33, B:K.99, B:G.100, B:D.108, A:G.92 MAN-MAN.2: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN-MAN.5: 11 residues within 4Å: Chain C: A.31, H.32, T.33, K.99, G.100, S.101, L.104, S.105, D.106, D.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.31, C:T.33, C:K.99, C:S.101, C:S.105, C:D.108, D:G.92 MAN-MAN.13: 11 residues within 4Å: Chain K: A.31, H.32, T.33, K.99, G.100, S.101, L.104, S.105, D.106, D.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.12 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain O Hydrogen bonds: K:A.31, K:T.33, K:K.99, K:S.101, K:S.105, K:D.108, O:G.92 MAN-MAN.14: 10 residues within 4Å: Chain N: G.92 Chain P: A.31, H.32, T.33, K.99, G.100, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN.7 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain N Hydrogen bonds: P:A.31, P:T.33, P:K.99, P:G.100, P:D.108, N:G.92 MAN-MAN.15: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) MAN-MAN.17: 10 residues within 4Å: Chain S: G.92 Chain T: A.31, H.32, T.33, K.99, G.100, D.106, N.107, D.108 Ligands: NAG-NAG-BMA-MAN.9 6 PLIP interactions: 5 interactions with chain T, 1 interactions with chain S Hydrogen bonds: T:A.31, T:T.33, T:K.99, T:G.100, T:D.108, S:G.92 MAN-MAN.18: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) MAN-MAN.21: 11 residues within 4Å: Chain U: A.31, H.32, T.33, K.99, G.100, S.101, L.104, S.105, D.106, D.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.20 7 PLIP interactions: 1 interactions with chain V, 6 interactions with chain U Hydrogen bonds: V:G.92, U:A.31, U:T.33, U:K.99, U:S.101, U:S.105, U:D.108

3 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.3: 3 residues within 4Å: Chain B: L.75, E.76 Chain C: T.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 NAG-NAG-BMA-MAN-MAN-MAN.16: 3 residues within 4Å: Chain K: T.56 Chain P: L.75, E.76 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.76 NAG-NAG-BMA-MAN-MAN-MAN.19: 3 residues within 4Å: Chain T: L.75, E.76 Chain U: T.56 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:E.76

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 2 residues within 4Å: Chain C: D.106 Ligands: MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 5 residues within 4Å: Chain C: F.27, R.28 Chain I: K.304, A.305 Ligands: MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 5 residues within 4Å: Chain E: K.304, A.305 Chain K: F.27, R.28 Ligands: MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.10: 5 residues within 4Å: Chain G: K.304, A.305 Chain U: F.27, R.28 Ligands: MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 2 residues within 4Å: Chain K: D.106 Ligands: MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.20: 2 residues within 4Å: Chain U: D.106 Ligands: MAN-MAN.21 No protein-ligand interaction detected (PLIP)

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(Non-functional Binders)

NAG-NAG-BMA-MAN.7: 1 residues within 4Å: Ligands: MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.9: 1 residues within 4Å: Ligands: MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.11: 1 residues within 4Å: Ligands: MAN-MAN.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuang, G.Y. et al., Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition. Structure (2019)

Release Date

2019-02-13

Peptides

2G12 Light chain: ADNOSV
2G12 heavy chain: BCKPTU
Envelope glycoprotein gp120: EGI
Envelope glycoprotein gp160: FHJ
VRC03 heavy chain: LQW
VRC03 Light chain: MRX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

D
4

N
K

O
L

S
Q

V
T

B
2

C
3

K
H

P
M

T
R

U
S

E
A

G
C

I
E

F
B

H
D

J
F

L
I

Q
O

W
V

M
J

R
P

X
W

2G12 Light chain

2G12 heavy chain

Envelope glycoprotein gp120

Envelope glycoprotein gp160

VRC03 heavy chain

VRC03 Light chain

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