SMTL ID : 5t3s.1

HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.50 Å

Oligo State

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

Ligands

3 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.1: 9 residues within 4Å: Chain A: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN-MAN.18: 9 residues within 4Å: Chain G: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.19 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.348 NAG-NAG-BMA-MAN-MAN-MAN-MAN.35: 9 residues within 4Å: Chain M: S.179, E.181, P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.36 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.348

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 A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: Q.332, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.204, S.244, I.247 Chain E: P.77 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain G: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain G: Q.332, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain G: N.204, S.244, I.247 Chain K: P.77 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.35 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 6 residues within 4Å: Chain M: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain M: Q.332, N.355, S.357 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain M: N.204, S.244, I.247 Chain Q: P.77 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.6: 5 residues within 4Å: Chain A: V.144, R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 5 residues within 4Å: Chain G: V.144, R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.40: 5 residues within 4Å: Chain M: V.144, R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP)

6 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.7: 4 residues within 4Å: Chain A: T.102, Y.104, N.118, S.120 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.8: 4 residues within 4Å: Chain A: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 4 residues within 4Å: Chain G: T.102, Y.104, N.118, S.120 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.25: 4 residues within 4Å: Chain G: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.41: 4 residues within 4Å: Chain M: T.102, Y.104, N.118, S.120 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.42: 4 residues within 4Å: Chain M: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP)

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.9: 20 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain E: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain F: H.95, N.96 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.115, E:T.115, E:D.111, E:G.112, F:H.95, E:H.33, E:D.111 NAG-NAG-BMA-MAN-MAN-MAN-MAN.26: 20 residues within 4Å: Chain G: E.57, N.58 Chain H: G.16, S.17 Chain K: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain L: H.95, N.96 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.115, K:T.115, L:H.95, K:D.111, K:G.112, K:H.33, K:D.111 NAG-NAG-BMA-MAN-MAN-MAN-MAN.43: 20 residues within 4Å: Chain M: E.57, N.58 Chain N: G.16, S.17 Chain Q: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, R.110, D.111, G.112, S.113, T.115 Chain R: H.95, N.96 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:T.115, Q:T.115, Q:D.111, Q:G.112, R:H.95, Q:H.33, Q:D.111

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.10: 20 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, R.412 Chain C: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain D: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.108 Hydrogen bonds: D:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.27: 20 residues within 4Å: Chain G: T.267, H.299, N.301, S.381, R.412 Chain I: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain J: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:V.108 Hydrogen bonds: J:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44: 20 residues within 4Å: Chain M: T.267, H.299, N.301, S.381, R.412 Chain O: S.25, N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain P: Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:V.108 Hydrogen bonds: P:V.108

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

NAG.11: 4 residues within 4Å: Chain A: S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.361 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: E.2 Chain B: N.105, N.107 Chain F: E.55, R.56 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain G: S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain G: N.361 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain G: E.2 Chain H: N.105, N.107 Chain L: E.55, R.56 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain M: S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain M: N.361 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain M: E.2 Chain N: N.105, N.107 Chain R: E.55, R.56 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steichen, J.M. et al., HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies. Immunity (2016)

Release Date

2016-09-28

Peptides

Envelope glycoprotein gp160: AGM
Envelope glycoprotein gp160: BHN
Fab PGT124 light chain: CIO
Fab PGT124 heavy chain: DJP
Fab 35022 heavy chain: EKQ
Fab 35022 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

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Fab PGT124 light chain

Fab PGT124 heavy chain

Fab 35022 heavy chain

Fab 35022 light chain

Related Entries With Identical Sequence