Structure summary for 2ZPK

Detailed entry information.

Key:

Heavy Chains
Light Chains
Bound Antigen Chains
Chothia CDRs
Other

Display options:
Spacefill model
Wire model
Ball&stick model
Cartoon model
Color atom number
Color by structure
Isosurface vdw: on off
Spin: on off

Crystal Structure Of P20.1 Fab Fragment In Complex With Its Antigen Peptide

ItemInfo
PDB code: 2zpk
Organism: MUS MUSCULUS
Experimental method: X-RAY DIFFRACTION
In complex: True
Fvs present: 2
Binding affinity (KD): 1.47e-06 M
ΔG: -7.95 kcal/mol
Affinity method: SPR
Temperature: 25 °C
Source: Paper Link
Light chain type: Lambda
PDB has constant region: True

This PDB has 2 antibody variable fragment(s)

Fab Details:
ItemInfo
Heavy Chain H
Light Chain L
Heavy V / J / C subgroups IGHV9 / IGHJ3 / IGHG1
Light V / J / C subgroups IGLV1 / IGLJ1 / IGLC1
Bound-state Bound
Species MUS MUSCULUS
ScFv? False
Constant domains present? True
Antigen Details:
ItemInfo
Chain P
Type peptide
Name proteinase-activated receptor 4
Species SYNTHETIC CONSTRUCT

Sequence:
Chain typeChain idFasta sequenceChothia annotated sequence ( framework / CDRs )
VH H Download
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10
EIQLVQSGPE
H11 H12 H13 H14 H15 H16 H17 H18 H19 H20
VQKPGETVRI
H21 H22 H23 H24 H25 H26 H27 H28 H29 H30
SCKASGYTFT
H31 H32 H33 H34 H35 H36 H37 H38 H39 H40
TAGMQWVQKM
H41 H42 H43 H44 H45 H46 H47 H48 H49 H50
PGKSLKWIGW
H51 H52 H52AH53 H54 H55 H56 H57 H58 H59
INTRSGVPKY
H60 H61 H62 H63 H64 H65 H66 H67 H68 H69
AEDFKGRFAF
H70 H71 H72 H73 H74 H75 H76 H77 H78 H79
SLETSASIAY
H80 H81 H82 H82AH82BH82CH83 H84 H85 H86
LHINNLKNED
H87 H88 H89 H90 H91 H92 H93 H94 H95 H96
TATYFCAREG
H97 H98 H99 H101 H102 H103 H104 H105 H106 H107
PGFVYWGQGT
H108 H109 H110 H111 H112 H113
LVTVSA
VL L Download
L1 L2 L3 L4 L5 L6 L7 L8 L9 L11
ETVVTQESAL
L12 L13 L14 L15 L16 L17 L18 L19 L20 L21
TTSPGETVTL
L22 L23 L24 L25 L26 L27 L28 L29 L30 L30A
TCRSSTGAVT
L30BL30CL31 L32 L33 L34 L35 L36 L37 L38
TSNYANWVQE
L39 L40 L41 L42 L43 L44 L45 L46 L47 L48
KPDHLFTGLI
L49 L50 L51 L52 L53 L54 L55 L56 L57 L58
VGTNNRVPGV
L59 L60 L61 L62 L63 L64 L65 L66 L67 L68
PPRFSGSLIG
L69 L70 L71 L72 L73 L74 L75 L76 L77 L78
DKAALTITGA
L79 L80 L81 L82 L83 L84 L85 L86 L87 L88
QTEDEAIYFC
L89 L90 L91 L92 L93 L94 L95 L96 L97 L98
ALWYSNHWVF
L99 L100 L101 L102 L103 L104 L105 L106 L106AL107
GGGTKLTVLG
L108 L109
QP
Antigen typeChain idFasta sequenceSequence (Clustal colouring)
peptide P Download
P R G Y P G Q V

Antibody i-Patch annotation:
Fab heavy/lightchainLink to the Antibody i-Patch annotation (What is this?)
H/LGet AB i-Patch annotation
Chothia CDR information:
CDRSequence
CDRL1 RSSTGAVTTSNYAN
CDRL2 GTNNRVP
CDRL3 ALWYSNHWV
CDRH1 GYTFTTA
CDRH2 NTRSGV
CDRH3 EGPGFVY
VH-VL orientation:
(see plot)
AngleValue
HL -61.1°
HC1 68.2°
HC2 110.3°
LC1 114.6°
LC2 86.7°
dc 15.7 Å
Fab Details:
ItemInfo
Heavy Chain I
Light Chain M
Heavy V / J / C subgroups IGHV9 / IGHJ3 / IGHG1
Light V / J / C subgroups IGLV1 / IGLJ1 / IGLC1
Bound-state Bound
Species MUS MUSCULUS
ScFv? False
Constant domains present? True
Antigen Details:
ItemInfo
Chain Q
Type peptide
Name proteinase-activated receptor 4
Species SYNTHETIC CONSTRUCT

Sequence:
Chain typeChain idFasta sequenceChothia annotated sequence ( framework / CDRs )
VH I Download
H1 H2 H3 H4 H5 H6 H7 H8 H9 H10
EIQLVQSGPE
H11 H12 H13 H14 H15 H16 H17 H18 H19 H20
VQKPGETVRI
H21 H22 H23 H24 H25 H26 H27 H28 H29 H30
SCKASGYTFT
H31 H32 H33 H34 H35 H36 H37 H38 H39 H40
TAGMQWVQKM
H41 H42 H43 H44 H45 H46 H47 H48 H49 H50
PGKSLKWIGW
H51 H52 H52AH53 H54 H55 H56 H57 H58 H59
INTRSGVPKY
H60 H61 H62 H63 H64 H65 H66 H67 H68 H69
AEDFKGRFAF
H70 H71 H72 H73 H74 H75 H76 H77 H78 H79
SLETSASIAY
H80 H81 H82 H82AH82BH82CH83 H84 H85 H86
LHINNLKNED
H87 H88 H89 H90 H91 H92 H93 H94 H95 H96
TATYFCAREG
H97 H98 H99 H101 H102 H103 H104 H105 H106 H107
PGFVYWGQGT
H108 H109 H110 H111 H112 H113
LVTVSA
VL M Download
L1 L2 L3 L4 L5 L6 L7 L8 L9 L11
ETVVTQESAL
L12 L13 L14 L15 L16 L17 L18 L19 L20 L21
TTSPGETVTL
L22 L23 L24 L25 L26 L27 L28 L29 L30 L30A
TCRSSTGAVT
L30BL30CL31 L32 L33 L34 L35 L36 L37 L38
TSNYANWVQE
L39 L40 L41 L42 L43 L44 L45 L46 L47 L48
KPDHLFTGLI
L49 L50 L51 L52 L53 L54 L55 L56 L57 L58
VGTNNRVPGV
L59 L60 L61 L62 L63 L64 L65 L66 L67 L68
PPRFSGSLIG
L69 L70 L71 L72 L73 L74 L75 L76 L77 L78
DKAALTITGA
L79 L80 L81 L82 L83 L84 L85 L86 L87 L88
QTEDEAIYFC
L89 L90 L91 L92 L93 L94 L95 L96 L97 L98
ALWYSNHWVF
L99 L100 L101 L102 L103 L104 L105 L106 L106AL107
GGGTKLTVLG
L108 L109
QP
Antigen typeChain idFasta sequenceSequence (Clustal colouring)
peptide Q Download
P R G Y P G Q V

Antibody i-Patch annotation:
Fab heavy/lightchainLink to the Antibody i-Patch annotation (What is this?)
I/MGet AB i-Patch annotation
Chothia CDR information:
CDRSequence
CDRL1 RSSTGAVTTSNYAN
CDRL2 GTNNRVP
CDRL3 ALWYSNHWV
CDRH1 GYTFTTA
CDRH2 NTRSGV
CDRH3 EGPGFVY
VH-VL orientation:
(see plot)
AngleValue
HL -64.7°
HC1 66.7°
HC2 109.7°
LC1 115.0°
LC2 84.9°
dc 16.2 Å

Downloads and links.

ItemDownload link
Full structureDownload
Chothia structureDownload
Summary fileDownload
Entry in the PDBSee the file on the PDB
Entry in IMGTSee the IMGT entry
Flag misannotation