8G82 | pdb_00008g82

Vancomycin bound to D-Ala-D-Ser

PDB DOI: https://doi.org/10.2210/pdb8G82/pdb

Classification: ANTIBIOTIC
Organism(s): Amycolatopsis orientalis, synthetic construct
Mutation(s): No

Deposited: 2023-02-17 Released: 2024-01-24
Deposition Author(s): Loll, P.J., Park, J.H.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.171 (Depositor), 0.171 (DCC)
R-Value Work:
0.153 (Depositor), 0.153 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of vancomycin bound to the resistance determinant D-alanine-D-serine.

Park, J.H., Reviello, R.E., Loll, P.J.

(2024) IUCrJ 11: 133-139

PubMed: 38277167 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2052252524000289
Primary Citation Related Structures:
8G82

PubMed Abstract:
Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to D-alanine-D-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the D-alanine-D-serine ligand is bound in essentially the same position and same pose as the native D-alanine-D-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups - one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic - are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, PA 19102, USA.

Macromolecule Content

Total Structure Weight: 17.44 kDa
Atom Count: 1,542
Modeled Residue Count: 100
Deposited Residue Count: 100
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vancomycin	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	7	Amycolatopsis orientalis	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Ala-D-Ser	K, L, M, N, O K, L, M, N, O, P, Q, R, S, T	3	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
vancosamine-(1-2)-beta-D-glucopyranose	AA [auth k], BA [auth m], U, V [auth W], W [auth Y], AA [auth k], BA [auth m], U, V [auth W], W [auth Y], X [auth a], Y [auth c], Z [auth e]	2		N/A	Interactions Focus chain AA [auth k] Focus chain BA [auth m] Focus chain U Focus chain V [auth W] Focus chain W [auth Y] Focus chain X [auth a] Focus chain Y [auth c] Focus chain Z [auth e] Interactions & Density Focus chain AA [auth k] Focus chain BA [auth m] Focus chain U Focus chain V [auth W] Focus chain W [auth Y] Focus chain X [auth a] Focus chain Y [auth c] Focus chain Z [auth e]
Glycosylation Resources
GlyTouCan: G14263HU GlyCosmos: G14263HU

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth H]	FA [auth G], JA [auth H]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain FA [auth G] Focus chain JA [auth H] Interactions & Density Focus chain FA [auth G] Focus chain JA [auth H]
RER Query on RER Download:Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain KA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain KA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain KA [auth H]	GA [auth G], KA [auth H]	vancosamine C₇ H₁₅ N O₃ OIJZDPGKNVKVBL-WNJXEPBRSA-N		Interactions Focus chain GA [auth G] Focus chain KA [auth H] Interactions & Density Focus chain GA [auth G] Focus chain KA [auth H]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain CA [auth A]	CA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Interactions & Density Focus chain CA [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain MA [auth J] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain MA [auth J] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain MA [auth J]	EA [auth G], HA [auth H], IA [auth H], MA [auth J]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain MA [auth J] Interactions & Density Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain MA [auth J]
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain LA [auth J] SDF format, chain NA [auth O] MOL2 format, chain DA [auth D] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth O] mmCIF format, chain DA [auth D] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth O]	DA [auth D], LA [auth J], NA [auth O]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain LA [auth J] Focus chain NA [auth O] Interactions & Density Focus chain DA [auth D] Focus chain LA [auth J] Focus chain NA [auth O]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG Query on 3FG	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₈ H₉ N O₄		--
GHP Query on GHP	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	D-PEPTIDE LINKING	C₈ H₉ N O₃		--
MLU Query on MLU	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	D-PEPTIDE LINKING	C₇ H₁₅ N O₂		--
OMY Query on OMY	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		TYR
OMZ Query on OMZ	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	D-PEPTIDE LINKING	C₉ H₁₀ Cl N O₄		--
DAL Query on DAL	K, L, M, N, O K, L, M, N, O, P, Q, R, S, T	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DSN Query on DSN	K, L, M, N, O K, L, M, N, O, P, Q, R, S, T	D-PEPTIDE LINKING	C₃ H₇ N O₃		--