SMTL ID : 5jxa.1

Crystal structure of ligand-free VRC03 antigen-binding fragment.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: G.107, S.108, C.109, P.116, Q.118 Chain B: L.45, Y.48, A.54, S.55 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.107, A:S.108, A:S.108, A:C.109 Water bridges: A:C.109 EDO.2: 10 residues within 4Å: Chain A: L.159, V.187, S.195, L.196, S.197 Chain B: V.128, Q.155, S.157, S.171, T.173 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:S.171, B:T.173, B:T.173, A:S.197, A:S.197 Hydrogen bonds: A:S.197, A:S.197 EDO.7: 8 residues within 4Å: Chain A: K.232 Chain B: P.114, Y.181, F.204, N.205, R.206, G.207, E.208 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.232, B:G.207

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: S.108, C.109, D.110, Y.111 Chain B: R.52 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.110 Water bridges: A:S.108, B:R.52 Salt bridges: B:R.52 PO4.8: 5 residues within 4Å: Chain B: E.182, K.183, H.184, K.185, R.206 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.185, B:R.206 Salt bridges: B:K.185, B:R.206 PO4.9: 4 residues within 4Å: Chain B: E.1, I.2, Q.27, F.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.1, B:Q.27, B:Q.27, B:Q.27

3 x CU: COPPER (II) ION(Non-covalent)

CU.4: 6 residues within 4Å: Chain A: G.180, H.182, T.201 Chain B: N.132, N.133, S.169 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.182, H2O.1, H2O.16 CU.5: 2 residues within 4Å: Chain B: D.146, H.184 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.146, B:H.184, H2O.16 CU.6: 7 residues within 4Å: Chain B: Q.36, R.38, R.44, R.60, F.61, E.80, D.81 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davenport, T.M. et al., Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies. Structure (2016)

Release Date

2016-07-27

Peptides

VRC03 Heavy chain: A
VRC03 Light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

VRC03 Heavy chain

VRC03 Light chain

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