6MET

Deposited: 2018-09-07 Released: 2018-12-12
Deposition Author(s): Shaik, M.M., Chen, B.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G]	461	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env Membrane Entity: Yes
UniProt
Find proteins for Q70145 (Human immunodeficiency virus 1) Explore Q70145 Go to UniProtKB: Q70145
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70145
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B [auth A]	363	Homo sapiens	Mutation(s): 0 Gene Names: CD4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730 Go to UniProtKB: P01730
PHAROS: P01730 GTEx: ENSG00000010610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01730
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C-C chemokine receptor type 5	C [auth B]	313	Homo sapiens	Mutation(s): 0 Gene Names: CCR5, CMKBR5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P51681 (Homo sapiens) Explore P51681 Go to UniProtKB: P51681
PHAROS: P51681 GTEx: ENSG00000160791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51681
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], G [auth F], H, I, K, D [auth C], G [auth F], H, I, K, L	2		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain G [auth F] Focus chain H Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain D [auth C] Focus chain G [auth F] Focus chain H Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], J	3		N-Glycosylation	Interactions Focus chain E [auth D] Focus chain J Interactions & Density Focus chain E [auth D] Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	F [auth E]	6		N-Glycosylation	Interactions Focus chain F [auth E] Interactions & Density Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain R [auth G] SDF format, chain S [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G]	M [auth G] N [auth G] O [auth G] P [auth G] Q [auth G] M [auth G], N [auth G], O [auth G], P [auth G], Q [auth G], R [auth G], S [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G] Interactions & Density Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth G] Focus chain S [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C [auth B]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2.1

Entry History & Funding Information

Deposition Author(s):

Shaik, M.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI141002

Version 1.0: 2018-12-12
Type: Initial release
Version 1.1: 2018-12-26
Changes: Data collection, Database references
Version 1.2: 2019-01-16
Changes: Data collection, Database references
Version 1.3: 2019-12-18
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary