SMTL ID : 7lua.1

Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-mer

Ligands

26 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: 9 residues within 4Å: Chain E: Q.323, S.348, N.349, N.352, G.353 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG-NAG-BMA-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 8 residues within 4Å: Chain E: E.53, V.55, K.189, N.191, D.192, E.193, S.202, N.203 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.53, E:N.191 NAG-NAG-BMA.5: 9 residues within 4Å: Chain E: A.104, T.105, V.106, N.116, S.118, Y.133, L.135, D.282, I.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 8 residues within 4Å: Chain E: Q.323, M.329, T.332, T.333, N.346, T.347, S.348 Ligands: NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 8 residues within 4Å: Chain E: V.257, T.259, K.288, H.291, N.293, S.370, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 12 residues within 4Å: Chain E: E.296, N.300, L.303, Q.304, Y.321, N.352, G.353, T.354, Y.355, I.360, N.363 Ligands: NAG-NAG-BMA.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.353 NAG-NAG-BMA.11: 8 residues within 4Å: Chain E: V.97, T.98, I.100, F.119, N.120, E.129, K.130, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain E: V.142, R.154, I.156, N.159, T.160 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 10 residues within 4Å: Chain A: K.320, Y.321, N.322, Q.323, N.352, G.353, T.354, T.425, R.427 Ligands: NAG-NAG-BMA.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 5 residues within 4Å: Chain A: Q.323, N.352, G.353 Ligands: NAG-NAG-BMA.15, NAG-NAG-BMA.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 6 residues within 4Å: Chain A: E.53, V.55, N.191, D.192, E.193, N.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.53 NAG-NAG-BMA.20: 12 residues within 4Å: Chain A: S.102, N.103, A.104, T.105, V.106, N.116, S.118, K.131, E.132, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 8 residues within 4Å: Chain A: T.333, Y.344, C.345, N.346, S.348, Q.375, C.376, R.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.346 NAG-NAG-BMA.23: 8 residues within 4Å: Chain A: V.257, T.259, H.291, N.293, S.370, T.371, T.373, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 13 residues within 4Å: Chain A: E.296, N.300, L.303, Q.304, Y.321, N.352, G.353, T.354, Y.355, I.360, T.362, N.363 Ligands: NAG-NAG-BMA.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.353, A:N.363 NAG-NAG-BMA.26: 6 residues within 4Å: Chain A: I.100, S.118, F.119, N.120, K.131, E.132 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain A: V.142, R.154, I.156, N.159, T.160 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 8 residues within 4Å: Chain C: K.320, N.322, Q.323, A.325, N.352, T.354, R.427 Ligands: NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 5 residues within 4Å: Chain C: N.352, G.353 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.37, NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 8 residues within 4Å: Chain C: E.53, V.55, K.189, N.191, D.192, E.193, N.203, K.230 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.53, C:N.191 NAG-NAG-BMA.33: 12 residues within 4Å: Chain C: S.102, N.103, A.104, T.105, V.106, N.116, S.118, K.131, Y.133, L.135, G.281, D.282 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.133 NAG-NAG-BMA.34: 10 residues within 4Å: Chain C: Q.323, T.332, T.333, Y.344, C.345, N.346, S.348, Q.375, C.376, R.377 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.346 NAG-NAG-BMA.36: 10 residues within 4Å: Chain C: V.257, T.259, P.261, K.288, H.291, N.293, T.371, T.373, T.402 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 13 residues within 4Å: Chain C: E.296, N.300, L.303, Q.304, Y.321, N.352, G.353, T.354, Y.355, I.360, N.363 Ligands: NAG-NAG-BMA.29, NAG-NAG-BMA.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.353 NAG-NAG-BMA.39: 7 residues within 4Å: Chain A: D.127 Chain C: V.97, T.98, I.100, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 6 residues within 4Å: Chain A: R.270 Chain C: V.142, R.154, I.156, N.159, T.160 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: 9 residues within 4Å: Chain E: W.66, N.196, T.198, G.199, I.234, R.235, S.236, L.239, T.240 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain E: N.263, N.264, T.265, I.284, G.399 Ligands: NAG.55 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.103, T.105, T.110, K.115, K.138 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 11 residues within 4Å: Chain A: N.62, M.65, W.66, N.196, G.197, T.198, G.199, P.200, R.235, S.236, E.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.198 NAG-NAG.22: 5 residues within 4Å: Chain A: N.263, T.265, I.284, G.399 Ligands: NAG.44 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain A: S.102, N.103, T.110, K.115, K.138, T.150 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 9 residues within 4Å: Chain C: W.66, N.196, G.197, T.198, G.199, S.236, E.237, N.238, L.239 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 7 residues within 4Å: Chain C: N.263, I.284, D.286, A.398, G.399, N.400 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain C: S.102, N.103, T.110, E.112, K.115 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN: 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.4: 17 residues within 4Å: Chain E: T.171, E.173, P.174, R.214, V.216, L.223, N.224, F.336, N.337, C.338, G.339, I.397, C.403, R.404, S.405, N.406 Ligands: NAG.54 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.173, E:E.173, E:G.339 NAG-NAG-BMA-MAN-MAN.14: 6 residues within 4Å: Chain E: N.238, T.240, N.241 Chain I: Y.33, K.52 Chain J: H.31 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:H.31, I:Y.33, I:K.52 NAG-NAG-BMA-MAN-MAN.19: 11 residues within 4Å: Chain A: E.173, P.174, V.216, L.223, N.224, N.337, C.403, R.404, S.405, N.406 Ligands: NAG.43 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.404 Hydrogen bonds: A:E.173, A:R.404 NAG-NAG-BMA-MAN-MAN.32: 12 residues within 4Å: Chain C: E.173, P.174, V.216, L.223, N.224, F.336, N.337, C.403, R.404, S.405, N.406 Ligands: NAG.49 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:R.404 Hydrogen bonds: C:E.173, C:R.404

1 x NAG- NAG- BMA- MAN- MAN- MAN: 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.13: 14 residues within 4Å: Chain E: K.320, N.322, G.353, R.427 Chain G: V.97, A.98 Chain H: Y.33, K.52, V.55, N.59, F.103, L.104 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP)

17 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.41: 6 residues within 4Å: Chain A: L.56, G.57, N.58 Chain B: A.7, G.9, S.10 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.238, T.240, N.241 Ligand excluded by PLIP NAG.43: 8 residues within 4Å: Chain A: N.224, L.227, P.253, E.255, R.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.19 Ligand excluded by PLIP NAG.44: 8 residues within 4Å: Chain A: R.260, P.261, N.262, N.263, G.399, N.400, T.402 Ligands: NAG-NAG.22 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.93, S.95, Y.120 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: R.99, K.115, E.116, S.118, N.119 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: L.56, G.57, N.58 Chain D: G.9, S.10 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.238, T.240, N.241, K.244 Ligand excluded by PLIP NAG.49: 9 residues within 4Å: Chain C: L.227, P.253, E.255, I.256, R.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.32, NAG-NAG-BMA-MAN-MAN.32 Ligand excluded by PLIP NAG.50: 13 residues within 4Å: Chain C: T.259, R.260, P.261, N.262, N.263, D.286, G.399, N.400, I.401, T.402 Ligands: NAG-NAG.35, NAG-NAG-BMA.36, NAG-NAG-BMA.36 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain D: N.93, S.95, Y.120, I.123 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: S.118, N.119, T.121 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: L.56, G.57, N.58 Chain F: S.10 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain E: N.224, P.253, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain E: P.261, N.263, N.400 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: N.93, S.95, Y.120 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain F: S.118, N.119, T.121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, W.B. et al., Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell (2021)

Release Date

2021-03-17

Peptides

CH848 SOSIP gp120: ACE
Env polyprotein: BDF
DH898.1 light chain: GJ
DH898.1 heavy chain: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

C
c

E
e

B
b

D
d

F
f

G
g

J
j

H
h

I
i

CH848 SOSIP gp120

Env polyprotein

DH898.1 light chain

DH898.1 heavy chain

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