SMTL ID : 5w6d.1

Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.1: 18 residues within 4Å: Chain A: R.289, H.292, N.294, S.374, T.376 Chain C: S.29, N.49, N.50, Q.51, P.65, D.66, I.67 Chain D: R.102, R.103, I.104, G.106, I.107, V.108 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.289, A:R.289, D:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13: 18 residues within 4Å: Chain G: R.289, H.292, N.294, S.374, T.376 Chain I: S.29, N.49, N.50, Q.51, P.65, D.66, I.67 Chain J: R.102, R.103, I.104, G.106, I.107, V.108 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain G Hydrogen bonds: J:V.108, G:R.289, G:R.289 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 18 residues within 4Å: Chain M: R.289, H.292, N.294, S.374, T.376 Chain O: S.29, N.49, N.50, Q.51, P.65, D.66, I.67 Chain P: R.102, R.103, I.104, G.106, I.107, V.108 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain P Hydrogen bonds: M:R.289, M:R.289, P:V.108

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.2: 20 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain E: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, D.57, K.58, R.110, D.111, G.112, S.113, T.115 Chain F: H.95, N.96 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.115, E:T.115, F:H.95, E:D.111, E:S.113, E:H.33, E:S.52, E:S.52 NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 20 residues within 4Å: Chain G: E.57, N.58 Chain H: G.16, S.17 Chain K: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, D.57, K.58, R.110, D.111, G.112, S.113, T.115 Chain L: H.95, N.96 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.115, K:T.115, K:D.111, K:S.113, L:H.95, K:H.33, K:S.52, K:S.52 NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 20 residues within 4Å: Chain M: E.57, N.58 Chain N: G.16, S.17 Chain Q: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, D.57, K.58, R.110, D.111, G.112, S.113, T.115 Chain R: H.95, N.96 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:T.115, Q:T.115, Q:D.111, Q:S.113, R:H.95, Q:H.33, Q:S.52, Q:S.52

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.3: 12 residues within 4Å: Chain A: K.34, S.172, P.175, V.217, N.225, N.339, C.340, G.341, C.406, V.407, S.408 Ligands: NAG-NAG-BMA-MAN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.341 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15: 12 residues within 4Å: Chain G: K.34, S.172, P.175, V.217, N.225, N.339, C.340, G.341, C.406, V.407, S.408 Ligands: NAG-NAG-BMA-MAN.16 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.341 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27: 12 residues within 4Å: Chain M: K.34, S.172, P.175, V.217, N.225, N.339, C.340, G.341, C.406, V.407, S.408 Ligands: NAG-NAG-BMA-MAN.28 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.341

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

NAG-NAG-BMA-MAN.4: 4 residues within 4Å: Chain A: L.228, P.254, N.409 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.16: 4 residues within 4Å: Chain G: L.228, P.254, N.409 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.28: 4 residues within 4Å: Chain M: L.228, P.254, N.409 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27 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.5: 6 residues within 4Å: Chain A: Q.256, N.258, N.294, V.295, S.296, R.405 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: N.197, T.199, P.201, S.237, I.240 Chain E: V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.264, I.285, V.403 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain G: Q.256, N.258, N.294, V.295, S.296, R.405 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain G: N.197, T.199, P.201, S.237, I.240 Chain K: V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain G: N.264, I.285, V.403 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 6 residues within 4Å: Chain M: Q.256, N.258, N.294, V.295, S.296, R.405 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 6 residues within 4Å: Chain M: N.197, T.199, P.201, S.237, I.240 Chain Q: V.78 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain M: N.264, I.285, V.403 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: 5 residues within 4Å: Chain A: V.104, N.118, S.120, H.135, D.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain G: V.104, N.118, S.120, H.135, D.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 5 residues within 4Å: Chain M: V.104, N.118, S.120, H.135, D.283 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain A: N.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.133, A:K.133 NAG.10: 3 residues within 4Å: Chain A: S.350, G.351, N.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.354 NAG.11: 4 residues within 4Å: Chain A: N.325, S.326, D.348, S.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.325 NAG.12: 2 residues within 4Å: Chain B: E.123, N.126 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.126 NAG.21: 1 residues within 4Å: Chain G: N.122 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.133, G:K.133 NAG.22: 3 residues within 4Å: Chain G: S.350, G.351, N.354 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.354 NAG.23: 4 residues within 4Å: Chain G: N.325, S.326, D.348, S.350 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.325 NAG.24: 2 residues within 4Å: Chain H: E.123, N.126 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:N.126 NAG.33: 1 residues within 4Å: Chain M: N.122 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:K.133, M:K.133 NAG.34: 3 residues within 4Å: Chain M: S.350, G.351, N.354 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.354 NAG.35: 4 residues within 4Å: Chain M: N.325, S.326, D.348, S.350 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.325 NAG.36: 2 residues within 4Å: Chain N: E.123, N.126 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:N.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina-Ramirez, M. et al., Design and crystal structure of a native-like HIV-1 envelope trimer that engages multiple broadly neutralizing antibody precursors in vivo. J. Exp. Med. (2017)

Release Date

2017-07-05

Peptides

BG505-SOSIP.v4.1-GT1-N137A gp120: AGM
BG505-SOSIP.v4.1-GT1-N137A gp41: BHN
109L FAB light chain: CIO
9H FAB heavy chain: DJP
35022 FAB heavy chain: EKQ
35022 FAB light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
G

M
G

B
B

H
B

N
B

C
L

I
L

O
L

D
H

J
H

P
H

E
D

K
D

Q
D

F
E

L
E

R
E

BG505-SOSIP.v4.1-GT1-N137A gp120

BG505-SOSIP.v4.1-GT1-N137A gp41

109L FAB light chain

9H FAB heavy chain

35022 FAB heavy chain

35022 FAB light chain

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